Phylota table contains all sequence, cluster and taxonomic information from a phylotaR pipeline run.

# S4 method for Phylota
as.character(x)

# S4 method for Phylota
show(object)

# S4 method for Phylota
print(x)

# S4 method for Phylota
str(object, max.level = 2L, ...)

# S4 method for Phylota
summary(object)

# S4 method for Phylota,character
[[(x, i)

Arguments

x

Phylota object

object

Phylota object

max.level

Maximum level of nesting for str()

...

Further arguments for str()

i

Either sid or cid

Slots

cids

IDs of all clusters

sids

IDs of all sequences

txids

IDs of all taxa

sqs

All sequence records as SeqArc

clstrs

All cluster records as ClstrArc

txdct

Taxonomic dictionary as TaxDict

prnt_id

Parent taxonomic ID

prnt_nm

Parent taxonomic name

See also

Examples

data('aotus') # this is a Phylota object # it contains cluster, sequence and taxonomic information from a phylotaR run show(aotus)
#> Phylota Table (Aotus) #> - [193] clusters #> - [1499] sequences #> - [13] source taxa
# you can access its different data slots with @ aotus@cids # cluster IDs
#> [1] "0" "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" #> [13] "12" "13" "14" "15" "16" "17" "18" "19" "20" "21" "22" "23" #> [25] "24" "25" "26" "27" "28" "29" "30" "31" "32" "33" "34" "35" #> [37] "36" "37" "38" "39" "40" "41" "42" "43" "44" "45" "46" "47" #> [49] "48" "49" "50" "51" "52" "53" "54" "55" "56" "57" "58" "59" #> [61] "60" "61" "62" "63" "64" "65" "66" "67" "68" "69" "70" "71" #> [73] "72" "73" "74" "75" "76" "77" "78" "79" "80" "81" "82" "83" #> [85] "84" "85" "86" "87" "88" "89" "90" "91" "92" "93" "94" "95" #> [97] "96" "97" "98" "99" "100" "101" "102" "103" "104" "105" "106" "107" #> [109] "108" "109" "110" "111" "112" "113" "114" "115" "116" "117" "118" "119" #> [121] "120" "121" "122" "123" "124" "125" "126" "127" "128" "129" "130" "131" #> [133] "132" "133" "134" "135" "136" "137" "138" "139" "140" "141" "142" "143" #> [145] "144" "145" "146" "147" "148" "149" "150" "151" "152" "153" "154" "155" #> [157] "156" "157" "158" "159" "160" "161" "162" "163" "164" "165" "166" "167" #> [169] "168" "169" "170" "171" "172" "173" "174" "175" "176" "177" "178" "179" #> [181] "180" "181" "182" "183" "184" "185" "186" "187" "188" "189" "190" "191" #> [193] "192"
aotus@sids # sequence IDs
#> [1] "FJ623078.1" "U38998.1" "U88361.1" #> [4] "AY684995.1" "AY684994.1" "AY684993.1" #> [7] "AY684992.1/1..1422" "AY684991.1/1..975" "U88362.1" #> [10] "U88363.1" "U88364.1" "AY227074.1" #> [13] "AY227073.1" "AY227072.1" "AY227071.1" #> [16] "AY227070.1" "AY227069.1" "AY227068.1" #> [19] "AY227067.1" "AY227066.1" "AY227065.1" #> [22] "AY227064.1" "AY227063.1" "AY227062.1" #> [25] "AY227061.1" "AY227060.1" "AY227059.1" #> [28] "AY227058.1" "AY227057.1" "AY227056.1" #> [31] "AY227055.1" "AY114513.1" "AF201297.1/23..790" #> [34] "AF201296.1/23..790" "AF201295.1/23..790" "AF201294.1/23..790" #> [37] "AF201293.1/23..790" "AF042146.1/11..370" "AF042146.1/371..877" #> [40] "AF042144.1/11..370" "AF042144.1/371..877" "GQ280000.1" #> [43] "GQ279969.1" "GQ279950.1" "GQ279948.1" #> [46] "GQ279925.1" "GQ279913.1" "GQ279878.1" #> [49] "GQ279859.1" "GQ279822.1" "GQ279802.1" #> [52] "GQ279784.1" "AY646198.1/152..1576" "AF420045.1/255..1619" #> [55] "DM461196.1" "DM461195.1" "DM461194.1" #> [58] "DM461193.1" "DM461192.1" "DM461191.1" #> [61] "DM367551.1" "DM367548.1" "DM367545.1" #> [64] "DM367544.1" "DM367543.1" "DM367542.1" #> [67] "DM367541.1" "DM367540.1" "DM371283.1" #> [70] "DM371280.1" "DM371276.1" "DM371275.1" #> [73] "DM371274.1" "DM371273.1" "DM371272.1" #> [76] "DM371271.1" "AB439577.1" "DQ200808.1" #> [79] "DQ334827.1" "AY449080.1" "AY449079.1" #> [82] "AY449071.1" "AY449070.1" "AY449069.1" #> [85] "AY449065.1" "AY449059.1" "AY449058.1" #> [88] "AY449057.1" "AY449013.1" "AY449012.1" #> [91] "AY449011.1" "AY449010.1" "AY449009.1" #> [94] "AY455163.1" "AY900569.1" "AY900568.1" #> [97] "AY900563.1" "AY900551.1" "AY900525.1" #> [100] "AY947712.1/543..825" "AB084909.2" "AB084908.2" #> [103] "AB084907.2" "AB081286.2" "AB081285.2" #> [106] "AB081284.2" "AB081283.2" "AB081282.2" #> [109] "AB081281.2" "AB081280.2" "AB081279.2" #> [112] "AB081278.2" "AB181216.1" "AB181215.1" #> [115] "AB181214.1/283..580" "AB181213.1" "AB181212.1" #> [118] "AB181211.1/463..760" "AB181210.1" "AB181209.1" #> [121] "AB181208.1/452..749" "AB181207.1" "AY225806.1" #> [124] "AY225805.1" "AY225802.1" "AY225801.1" #> [127] "AY225800.1" "AY225797.1" "AJ489745.1" #> [130] "AJ489746.1" "AB107211.1" "AY246458.1" #> [133] "AF489256.1/1..298" "AF489244.1/762..1058" "AY055463.1" #> [136] "AF286383.1" "U52114.1" "AB023939.1" #> [139] "AB023938.1" "AB023937.1" "HM756917.1" #> [142] "HM756916.1" "HM756841.1" "HM756840.1" #> [145] "HM756839.1" "HM756838.1" "HM757001.1" #> [148] "HM757000.1" "HM756999.1" "HM757384.1" #> [151] "HM757383.1" "HM757382.1" "HM757381.1" #> [154] "HM757380.1" "HM757379.1" "HM757559.1" #> [157] "HM757558.1" "HM757557.1" "HM757556.1" #> [160] "HM757555.1" "HM757554.1" "HM757725.1" #> [163] "HM757724.1" "HM757723.1" "HM757722.1" #> [166] "HM757721.1" "HM757720.1" "HM757999.1" #> [169] "HM758217.1" "HM758216.1" "HM758215.1" #> [172] "HM758214.1" "HM758213.1" "HM758212.1" #> [175] "HM758450.1" "HM758304.1" "HM758303.1" #> [178] "HM758302.1" "HM758297.1" "HM758295.1" #> [181] "HM758476.1" "HM758475.1" "HM758466.1" #> [184] "HM758465.1" "HM758464.1" "HM758463.1" #> [187] "HM758660.1" "HM758659.1" "HM758658.1" #> [190] "HM758657.1" "HM758656.1" "HM758655.1" #> [193] "HM758650.1" "HM758648.1" "HM758935.1" #> [196] "HM758934.1" "HM758933.1" "HM758932.1" #> [199] "HM758931.1" "HM758930.1" "HM759106.1" #> [202] "HM759105.1" "HM759104.1" "HM759103.1" #> [205] "HM759102.1" "HM759101.1" "HM759279.1" #> [208] "HM759278.1" "HM759277.1" "HM759276.1" #> [211] "HM759275.1" "HM759274.1" "HM759273.1" #> [214] "HM759535.1" "HM759379.1" "HM759378.1" #> [217] "HM759377.1" "HM759372.1" "HM759370.1" #> [220] "HM759647.1" "HM759646.1" "HM759645.1" #> [223] "HM759644.1" "HM759643.1" "HM759641.1" #> [226] "HM759836.1" "HM759819.1" "HM759777.1" #> [229] "HM759775.1" "HM759730.1" "HM759729.1" #> [232] "HM760059.1" "HM759903.1" "HM759902.1" #> [235] "HM759901.1" "HM759896.1" "HM759894.1" #> [238] "HM760239.1" "HM760087.1" "HM760086.1" #> [241] "HM760085.1" "HM760080.1" "HM760078.1" #> [244] "HM760421.1" "HM760263.1" "HM760262.1" #> [247] "HM760261.1" "HM760256.1" "HM760254.1" #> [250] "HM760530.1" "HM760529.1" "HM760528.1" #> [253] "HM760527.1" "HM760526.1" "HM760525.1" #> [256] "HM760759.1" "HM760615.1" "HM760614.1" #> [259] "HM760613.1" "HM760608.1" "HM760606.1" #> [262] "HM760776.1" "HM760775.1" "HM760774.1" #> [265] "HM761014.1" "HM761013.1" "HM761012.1" #> [268] "HM761011.1" "HM761146.1" "HM761145.1" #> [271] "HM761144.1" "HM761143.1" "HM761207.1" #> [274] "HM761206.1" "HM761196.1" "HM761195.1" #> [277] "HM761194.1" "HM761193.1" "HM761664.1" #> [280] "HM761514.1" "HM761513.1" "HM761512.1" #> [283] "HM761507.1" "HM761505.1" "HM761773.1" #> [286] "HM761772.1" "HM761771.1" "HM761770.1" #> [289] "HM761769.1" "HM761768.1" "HM761930.1" #> [292] "HM761929.1" "HM761928.1" "HM761927.1" #> [295] "HM761926.1" "HM761925.1" "HM762097.1" #> [298] "HM762096.1" "HM762095.1" "HM762094.1" #> [301] "HM762093.1" "HM762092.1" "HM762324.1" #> [304] "HM762245.1" "HM762207.1" "HM762199.1" #> [307] "HM762181.1" "HM762180.1" "HM762432.1" #> [310] "HM762431.1" "HM762430.1" "HM762429.1" #> [313] "HM762428.1" "HM762427.1" "HM762674.1" #> [316] "HM762517.1" "HM762516.1" "HM762511.1" #> [319] "HM762509.1" "HM762770.1" "HM762769.1" #> [322] "HM762768.1" "HM762767.1" "HM762766.1" #> [325] "HM762765.1" "HM762863.1" "HM762862.1" #> [328] "HM762858.1" "HM762856.1" "HM763022.1" #> [331] "HM763021.1" "HM763020.1" "HM763019.1" #> [334] "HM763266.1" "HM763265.1" "HM763264.1" #> [337] "HM763263.1" "HM763262.1" "HM763261.1" #> [340] "HM763434.1" "HM763433.1" "HM763432.1" #> [343] "HM763431.1" "HM763430.1" "HM763429.1" #> [346] "HM763505.1" "HM763504.1" "HM763503.1" #> [349] "HM763727.1" "HM763726.1" "HM763725.1" #> [352] "HM763724.1" "HM763723.1" "HM763722.1" #> [355] "HM763846.1" "HM763845.1" "HM763844.1" #> [358] "HM763997.1" "HM763996.1" "HM763995.1" #> [361] "HM763994.1" "HM764215.1" "HM764188.1" #> [364] "HM764187.1" "HM764105.1" "HM764104.1" #> [367] "HM764102.1" "HM764322.1" "HM764321.1" #> [370] "HM764320.1" "HM764319.1" "HM764318.1" #> [373] "HM764317.1" "HM764402.1" "HM764401.1" #> [376] "HM764396.1" "HM764394.1" "HM764649.1" #> [379] "HM764648.1" "HM764647.1" "HM764646.1" #> [382] "HM764645.1" "HM764817.1" "HM764816.1" #> [385] "HM764815.1" "HM764814.1" "HM764813.1" #> [388] "HM765068.1" "HM764910.1" "HM764909.1" #> [391] "HM764908.1" "HM764903.1" "HM764901.1" #> [394] "HM765180.1" "HM765179.1" "HM765178.1" #> [397] "HM765177.1" "HM765176.1" "HM765175.1" #> [400] "AB181223.1/324..589" "AB181222.1/324..589" "AB181222.1/1555..1849" #> [403] "AB181217.1/324..590" "AB181217.1/1545..1839" "FJ638418.1" #> [406] "FJ638417.1" "FJ638416.1" "FJ638415.1" #> [409] "FJ638414.1" "JQ932362.1" "JQ932359.1" #> [412] "JQ932356.1" "JQ932319.1" "JQ932318.1" #> [415] "JQ932310.1" "JQ932304.1" "JQ932303.1" #> [418] "JQ932293.1" "JQ932280.1" "JQ932259.1" #> [421] "JQ932255.1" "JQ932245.1" "JQ932232.1" #> [424] "DQ098868.1" "DQ098867.1" "AY455164.1" #> [427] "AY455162.1" "AY455159.1" "AY455158.1" #> [430] "AY455153.1" "AF169487.1" "AF169486.1" #> [433] "AF169485.1" "AF042145.1/1..355" "AF042145.1/356..862" #> [436] "U59646.1" "U59645.1" "U59644.1" #> [439] "U36845.1" "U36844.1" "U36843.1" #> [442] "U36846.1" "U36770.1" "JF444279.1" #> [445] "JN161098.1" "JN161097.1" "JN161096.1" #> [448] "JN161095.1" "JN161094.1" "JN161093.1" #> [451] "JN161092.1" "JN161091.1" "JN161090.1" #> [454] "JN161089.1" "JN161088.1" "JN161087.1" #> [457] "JN161086.1" "JN161085.1" "JN161084.1" #> [460] "JN161083.1" "JN161082.1" "JN161081.1" #> [463] "JN161080.1" "JN161079.1" "JN161078.1" #> [466] "JN161077.1" "JN161076.1" "JN161075.1" #> [469] "JN161074.1" "JN161073.1" "JN161072.1" #> [472] "JN161071.1" "JN161070.1" "JN161069.1" #> [475] "JQ932775.1" "JQ932756.1" "JQ932751.1" #> [478] "JQ932724.1" "JQ932717.1" "JQ932662.1" #> [481] "JQ932636.1" "JQ932630.1" "JQ932605.1" #> [484] "JQ932597.1" "JQ932590.1" "JQ933099.1" #> [487] "JQ933082.1" "JQ933076.1" "JQ933075.1" #> [490] "JQ933053.1" "JQ933029.1" "JQ933028.1" #> [493] "JQ933027.1" "JQ933026.1" "JQ933023.1" #> [496] "JQ933020.1" "JQ933011.1" "JQ933006.1" #> [499] "JQ933005.1" "JQ933004.1" "JQ933001.1" #> [502] "JQ933000.1" "JQ932999.1" "JQ932998.1" #> [505] "JQ932997.1" "JQ932996.1" "JQ932995.1" #> [508] "JQ932994.1" "JQ932993.1" "JQ932992.1" #> [511] "JQ932991.1" "JQ932990.1" "JQ932989.1" #> [514] "JQ932988.1" "JQ932987.1" "JQ932986.1" #> [517] "JQ932985.1" "JQ932984.1" "JQ932983.1" #> [520] "JQ932982.1" "JQ932981.1" "JQ932980.1" #> [523] "JQ932979.1" "JQ932978.1" "JQ932977.1" #> [526] "JQ932976.1" "JQ932975.1" "JQ932974.1" #> [529] "JQ932973.1" "JQ932972.1" "JQ932971.1" #> [532] "JQ932970.1" "JQ932969.1" "JQ932967.1" #> [535] "JQ932966.1" "JQ932965.1" "JQ932964.1" #> [538] "JQ932963.1" "JQ932962.1" "JQ932961.1" #> [541] "JQ932960.1" "JQ932959.1" "JQ932958.1" #> [544] "JQ932957.1" "JQ932956.1" "JQ932955.1" #> [547] "JQ932954.1" "JQ932953.1" "JQ932934.1" #> [550] "JQ932933.1" "JQ932932.1" "JQ932931.1" #> [553] "JQ932930.1" "JQ932929.1" "JQ932928.1" #> [556] "JQ932927.1" "JQ932926.1" "JQ932925.1" #> [559] "JQ932924.1" "JQ932923.1" "JQ932922.1" #> [562] "JQ932921.1" "JQ932920.1" "JQ932918.1" #> [565] "JQ932916.1" "JQ932914.1" "JQ932913.1" #> [568] "JQ932909.1" "JQ932908.1" "JQ932905.1" #> [571] "JQ932903.1" "JQ932897.1" "JQ932896.1" #> [574] "JQ932895.1" "JQ932892.1" "JQ932891.1" #> [577] "JQ932890.1" "JQ932889.1" "JQ932888.1" #> [580] "JQ932887.1" "JQ932886.1" "JQ932885.1" #> [583] "JQ932884.1" "JQ932882.1" "JQ932881.1" #> [586] "JQ932880.1" "JQ932879.1" "JQ932877.1" #> [589] "JQ932874.1" "JQ932873.1" "JQ932872.1" #> [592] "JQ932870.1" "JQ932869.1" "JQ932868.1" #> [595] "JQ932867.1" "JQ932866.1" "JQ932865.1" #> [598] "JQ932864.1" "JQ932863.1" "JQ932862.1" #> [601] "JQ932861.1" "JQ932859.1" "JQ932857.1" #> [604] "JQ932856.1" "JQ932855.1" "JQ932854.1" #> [607] "JQ932853.1" "JQ932852.1" "JQ932851.1" #> [610] "JQ932850.1" "JQ932849.1" "JQ932847.1" #> [613] "JQ932846.1" "JQ932845.1" "JQ932844.1" #> [616] "JQ932843.1" "JQ932842.1" "JQ932841.1" #> [619] "JQ932840.1" "JQ932839.1" "JQ932838.1" #> [622] "JQ932837.1" "JQ932836.1" "JQ932835.1" #> [625] "JQ932833.1" "JQ932831.1" "JQ932830.1" #> [628] "JQ932829.1" "JQ932827.1" "JQ932823.1" #> [631] "JQ932822.1" "JQ932821.1" "JQ932818.1" #> [634] "JQ932817.1" "JQ932816.1" "JQ932815.1" #> [637] "JQ932814.1" "JQ932813.1" "JQ932812.1" #> [640] "JQ932809.1" "JQ932807.1" "JQ932806.1" #> [643] "JQ932805.1" "JQ932804.1" "JQ932803.1" #> [646] "JQ932802.1" "JQ932801.1" "JQ932800.1" #> [649] "JQ932799.1" "JQ932794.1" "KC760418.1" #> [652] "KC760417.1" "KC760388.1" "KC760387.1" #> [655] "KC760386.1" "KC760385.1" "KC760329.1" #> [658] "KC760328.1" "KC760327.1" "KC760326.1" #> [661] "KC760297.1" "KC760296.1" "KC760295.1" #> [664] "KC760266.1" "KC760265.1" "KC760264.1" #> [667] "KC760263.1" "KC760231.1" "KC760230.1" #> [670] "KC760229.1" "KC760228.1" "AB762011.1" #> [673] "AB762010.1" "AB762009.1" "AB762008.1" #> [676] "AB762007.1" "AB762006.1" "AB762005.1" #> [679] "AB762004.1" "AB762003.1" "AB762002.1" #> [682] "AB762001.1" "AB762000.1" "AB761999.1" #> [685] "AB761998.1" "AB761997.1" "AB761996.1" #> [688] "AB761995.1" "AB761994.1" "AB761993.1" #> [691] "AB761992.1" "AB761991.1" "AB761990.1" #> [694] "AB761989.1" "AB761988.1" "AB761987.1" #> [697] "AB761986.1" "HW478260.1" "HW478259.1" #> [700] "HW478258.1" "HW478257.1" "HW478256.1" #> [703] "HW478255.1" "KF014088.1" "KF014089.1" #> [706] "KF014091.1/1..1059" "KF014090.1/1..1059" "KF014094.1" #> [709] "KF014093.1" "KF014092.1" "KF014098.1/1..1017" #> [712] "KF014097.1/1..1122" "KF014096.1/1..1209" "KF014095.1/1..1104" #> [715] "KF014103.1" "KF014102.1" "KF014101.1" #> [718] "KF014100.1" "KF014099.1/1..1332" "KF014105.1/1..1113" #> [721] "KF014104.1" "KF014106.1/1..1212" "KF014108.1/1..927" #> [724] "KF014107.1/1..1014" "KF014109.1" "KF014110.1/1..1110" #> [727] "KF014113.1" "KF014112.1" "KF014111.1" #> [730] "KF014116.1" "KF014115.1" "KF014114.1" #> [733] "KF014117.1/1..1263" "KF014118.1" "KF014119.1" #> [736] "KF014120.1/1..1395" "KF014122.1/1..978" "KF014121.1/1..1110" #> [739] "DI178960.1" "DI178959.1" "DI178958.1" #> [742] "DI178957.1" "DI178956.1" "DI178955.1" #> [745] "DI178127.1" "DI178124.1" "DI178120.1" #> [748] "DI178119.1" "DI178118.1" "DI178117.1" #> [751] "DI178116.1" "DI178115.1" "AB239248.1" #> [754] "AB239247.1" "AB239246.1" "AB239228.1" #> [757] "AB239227.1" "AB239226.1" "AB239203.1" #> [760] "AB239202.1" "AB239201.1" "AB239200.1" #> [763] "JQ963361.1" "JQ963360.1" "JQ963351.1" #> [766] "JQ963350.1" "JQ963349.1" "JQ963348.1" #> [769] "JQ963347.1" "JQ963346.1" "JQ933101.1" #> [772] "AY114530.1" "AY114529.1" "AY114528.1" #> [775] "AY114527.1" "AY114526.1" "AY114525.1" #> [778] "AY114524.1" "AY114523.1" "AY114522.1" #> [781] "AY114521.1" "AY114520.1" "AY114519.1" #> [784] "AY114518.1" "AY114517.1" "AY114516.1" #> [787] "AY114515.1" "AY114514.1" "AF486450.1" #> [790] "AF486449.1" "AF486448.1" "AF181085.1" #> [793] "AF004921.1" "AF027569.1" "AF027567.1" #> [796] "AF027566.1" "AF027565.1" "AF027564.1" #> [799] "AF027563.1" "AF027562.1" "AF027561.1/1..298" #> [802] "AF027560.1" "AF027559.1" "AF027554.1/1..256" #> [805] "AF027553.1" "AF027552.1" "AF027551.1" #> [808] "AF027549.1" "AF027548.1" "AF027547.1" #> [811] "AF027546.1/1..274" "AF027545.1" "AF027544.1" #> [814] "AF027543.1/1..265" "AF027542.1" "EF658656.1" #> [817] "EF658655.1" "EF658654.1" "EF658653.1" #> [820] "EF658652.1" "DQ989366.1" "AH006732.3/455..733" #> [823] "AH006511.2/455..733" "KR528418.1/1..1140" "KM206808.1" #> [826] "KM206805.1" "KM206804.1" "KC762196.1" #> [829] "KC762195.1" "KC762194.1" "KC762193.1" #> [832] "KC762163.1" "KC762162.1" "KC762161.1" #> [835] "KC762160.1" "KC762129.1" "KC762128.1" #> [838] "KC762127.1" "KC762106.1" "KC762105.1" #> [841] "KC762104.1" "KC762075.1" "KC762074.1" #> [844] "KC762073.1" "KC762072.1" "KC762017.1" #> [847] "KC762016.1" "KC762015.1" "KC762014.1" #> [850] "KC761983.1" "KC761982.1" "KC761981.1" #> [853] "KC761980.1" "KC761954.1" "KC761953.1" #> [856] "KC761952.1" "KC761951.1" "KC761921.1" #> [859] "KC761920.1" "KC761919.1" "KC761918.1" #> [862] "KC761892.1" "KC761891.1" "KC761890.1" #> [865] "KC761889.1" "KC761836.1" "KC761835.1" #> [868] "KC761834.1" "KC761833.1" "KC761816.1" #> [871] "KC761815.1" "KC761814.1" "KC761813.1" #> [874] "KC761785.1" "KC761784.1" "KC761783.1" #> [877] "KC761782.1" "KC761757.1" "KC761756.1" #> [880] "KC761755.1" "KC761698.1" "KC761697.1" #> [883] "KC761696.1" "KC761695.1" "KC761635.1" #> [886] "KC761634.1" "KC761633.1" "KC761632.1" #> [889] "KC761604.1" "KC761603.1" "KC761602.1" #> [892] "KC761601.1" "KC761572.1" "KC761571.1" #> [895] "KC761570.1" "KC761569.1" "KC761540.1" #> [898] "KC761539.1" "KC761538.1" "KC761537.1" #> [901] "KC761507.1" "KC761506.1" "KC761505.1" #> [904] "KC761504.1" "KC761473.1" "KC761472.1" #> [907] "KC761471.1" "KC761470.1" "KC761440.1" #> [910] "KC761439.1" "KC761438.1" "KC761408.1" #> [913] "KC761407.1" "KC761406.1" "KC761405.1" #> [916] "KC761373.1" "KC761372.1" "KC761371.1" #> [919] "KC761340.1" "KC761339.1" "KC761338.1" #> [922] "KC761279.1" "KC761278.1" "KC761277.1" #> [925] "KC761245.1" "KC761244.1" "KC761243.1" #> [928] "KC761242.1" "KC761212.1" "KC761211.1" #> [931] "KC761210.1" "KC761180.1" "KC761179.1" #> [934] "KC761178.1" "KC761177.1" "KC761146.1" #> [937] "KC761145.1" "KC761144.1" "KC761112.1" #> [940] "KC761111.1" "KC761083.1" "KC761082.1" #> [943] "KC761081.1" "KC761080.1" "KC761053.1" #> [946] "KC761052.1" "KC761051.1" "KC761050.1" #> [949] "KC761019.1" "KC761018.1" "KC761017.1" #> [952] "KC761016.1" "KC760991.1" "KC760990.1" #> [955] "KC760989.1" "KC760988.1" "KC760957.1" #> [958] "KC760956.1" "KC760955.1" "KC760954.1" #> [961] "KC760922.1" "KC760921.1" "KC760920.1" #> [964] "KC760894.1" "KC760893.1" "KC760892.1" #> [967] "KC760891.1" "KC760869.1" "KC760868.1" #> [970] "KC760867.1" "KC760866.1" "KC760836.1" #> [973] "KC760835.1" "KC760834.1" "KC760833.1" #> [976] "KC760805.1" "KC760804.1" "KC760803.1" #> [979] "KC760802.1" "KC760772.1" "KC760771.1" #> [982] "KC760770.1" "KC760741.1" "KC760740.1" #> [985] "KC760739.1" "KC760738.1" "KC760715.1" #> [988] "KC760714.1" "KC760713.1" "KC760712.1" #> [991] "KC760684.1" "KC760683.1" "KC760682.1" #> [994] "KC760681.1" "KC760649.1" "KC760648.1" #> [997] "KC760647.1" "KC760646.1" "KC760614.1" #> [1000] "KC760613.1" #> [ reached getOption("max.print") -- omitted 499 entries ]
aotus@txids # taxonomic IDs
#> [1] "37293" "9505" "57176" "57175" "43147" "231953" "30591" #> [8] "280755" "867331" "292213" "1002694" "120088" "361674"
aotus@clstrs # clusters archive
#> Archive of cluster record(s) #> - [193] clusters
aotus@sqs # sequence archive
#> Archive of sequence record(s) #> - [1499] sequences #> - [13] unique txids #> - [548] median sequence length #> - [0] median ambiguous nucleotides
aotus@txdct # taxonomic dictionary
#> Taxonomic dictionary [21] recs, parent [id 9504]
# see all of the available slots (slotNames(aotus))
#> [1] "cids" "txids" "sids" "txdct" "sqs" "clstrs" "prnt_id" #> [8] "prnt_nm"
# access different sequences and clusters with [[ (aotus[['0']]) # cluster record 0
#> Cluster Record [id 0] #> - [subtree] type #> - [AF129794.1] seed sequence #> - [204] sequences #> - [5] taxa
(aotus[[aotus@sids[[1]]]]) # first sequence record
#> SeqRec [ID: FJ623078.1]
# get a summary of the whole object (summary(aotus))
#> ID Type Seed Parent N_taxa N_seqs Med_sql MAD #> 1 0 subtree AF129794.1 9504 5 204 267.0 0.7124669 #> 2 1 subtree U52114.1 9504 5 63 1020.0 0.7604098 #> 3 2 subtree DI178118.1 9504 2 52 267.0 0.8666904 #> 4 3 subtree JQ932794.1 9504 4 43 568.0 0.6643121 #> 5 4 subtree U36844.1 9504 9 41 549.0 0.8397112 #> 6 5 subtree KF014117.1/1..1263 9504 1 35 1281.0 0.7731248 #> 7 6 subtree LC075891.1 9504 2 33 838.0 0.8026216 #> 8 7 subtree JN161069.1 9504 1 30 1088.0 0.9985614 #> 9 8 subtree JN161069.1 30591 1 30 1088.0 0.9985614 #> 10 9 subtree AJ489745.1 9504 10 29 1140.0 1.0000000 #> 11 10 subtree AF333711.1 9504 1 28 394.0 0.9228029 #> 12 11 direct LC075891.1 30591 1 26 839.0 0.8095820 #> 13 12 subtree JQ932884.1 9504 4 24 760.0 0.7909620 #> 14 13 subtree AF378747.1 9504 1 20 364.0 0.8938575 #> 15 14 subtree JQ932881.1 9504 4 19 521.0 0.7978981 #> 16 15 subtree AY900546.1 9504 1 19 290.0 0.6804250 #> 17 16 subtree JQ932999.1 9504 1 18 633.0 0.6914067 #> 18 17 subtree AF027542.1 9504 1 18 287.0 0.8037759 #> 19 18 subtree AF333712.1 9504 1 18 378.0 0.9713542 #> 20 19 subtree JQ932845.1 9504 4 17 588.0 0.6802310 #> 21 20 subtree JQ933027.1 9504 2 16 789.5 0.8442383 #> 22 21 subtree JQ932800.1 9504 4 14 633.0 0.7108335 #> 23 22 subtree DQ321662.1 30591 2 13 549.0 0.8050398 #> 24 23 subtree JQ932874.1 9504 1 12 543.5 0.8983452 #> 25 24 subtree KY508404.1 9504 1 12 411.5 0.9586317 #> 26 25 subtree JQ932840.1 9504 1 11 565.0 0.8977661 #> 27 26 subtree AF107750.1 9504 1 11 323.0 0.9789997 #> 28 27 direct AB761995.1 30591 1 11 785.0 0.8737194 #> 29 28 subtree JQ932868.1 9504 2 10 561.0 0.7707880 #> 30 29 subtree AF338374.1/177..829 9504 8 10 653.0 0.9658499 #> 31 30 subtree LC075890.1 9504 2 10 853.5 0.8719880 #> 32 31 subtree AY972694.1 9504 4 10 629.0 0.9725881 #> 33 32 subtree AY894647.1 9504 1 10 1170.0 0.9992314 #> 34 33 subtree JQ932807.1 9504 1 9 637.0 0.7393674 #> 35 34 subtree AF042144.1/11..370 9504 3 8 326.0 0.8920139 #> 36 35 subtree AY900559.1 9504 1 8 280.0 0.7162162 #> 37 36 subtree HM758648.1 9504 6 8 680.0 0.9605078 #> 38 37 subtree JQ932913.1 9504 1 7 754.0 0.8016142 #> 39 38 subtree AY449013.1 9504 1 7 685.0 1.0000000 #> 40 39 subtree AY900538.1 9504 1 7 315.0 0.9235474 #> 41 40 subtree HM759273.1 9504 6 7 715.0 0.9858142 #> 42 41 direct AY449013.1 30591 1 7 685.0 1.0000000 #> 43 42 direct EF658652.1 30591 1 7 629.0 0.9754224 #> 44 43 subtree DQ098867.1 30591 2 7 1140.0 1.0000000 #> 45 44 subtree NM_001308532.1/14..457 9504 4 6 465.0 0.9698925 #> 46 45 subtree AY646198.1/152..1576 9504 1 6 1405.5 0.8877193 #> 47 46 subtree AF201293.1/23..790 9504 1 6 768.0 1.0000000 #> 48 47 subtree GQ279878.1 9504 4 6 663.0 0.8277405 #> 49 48 subtree KC761051.1 9504 4 6 473.5 0.6922778 #> 50 49 subtree GQ279822.1 9504 4 6 578.0 0.7239464 #> 51 50 subtree HM756838.1 9504 6 6 552.0 0.9782738 #> 52 51 subtree HM757379.1 9504 6 6 612.0 0.9945534 #> 53 52 subtree HM757554.1 9504 6 6 475.0 0.9361404 #> 54 53 subtree HM757720.1 9504 6 6 899.0 0.9713971 #> 55 54 subtree HM758212.1 9504 6 6 341.0 0.9961014 #> 56 55 subtree HM758295.1 9504 6 6 636.0 0.9873776 #> 57 56 subtree HM758463.1 9504 6 6 590.0 0.9818182 #> 58 57 subtree HM758930.1 9504 6 6 505.5 0.7809254 #> 59 58 subtree HM759101.1 9504 6 6 1077.0 0.9996905 #> 60 59 subtree HM759370.1 9504 6 6 611.0 0.9763458 #> 61 60 subtree HM759641.1 9504 6 6 323.0 0.9343434 #> 62 61 subtree HM759729.1 9504 6 6 355.0 0.9737089 #> 63 62 subtree HM759894.1 9504 6 6 579.0 0.9408517 #> 64 63 subtree HM760078.1 9504 6 6 585.5 0.9216172 #> 65 64 subtree HM760254.1 9504 6 6 538.0 0.9959877 #> 66 65 subtree HM760525.1 9504 6 6 555.5 0.9838420 #> 67 66 subtree HM760606.1 9504 6 6 660.0 0.9917044 #> 68 67 subtree HM761193.1 9504 6 6 617.0 0.9767565 #> 69 68 subtree HM761505.1 9504 6 6 552.5 0.9365910 #> 70 69 subtree HM761768.1 9504 6 6 475.5 0.9530271 #> 71 70 subtree HM761925.1 9504 6 6 714.5 0.9683830 #> 72 71 subtree HM762092.1 9504 6 6 719.5 0.9822404 #> 73 72 subtree HM762180.1 9504 6 6 761.0 0.9868594 #> 74 73 subtree HM762427.1 9504 6 6 958.5 0.9632826 #> 75 74 subtree HM762765.1 9504 6 6 602.0 0.9706840 #> 76 75 subtree HM763261.1 9504 6 6 1000.0 0.9960000 #> 77 76 subtree HM763429.1 9504 6 6 399.0 0.9473039 #> 78 77 subtree HM763727.1 9504 6 6 1245.0 0.9453793 #> 79 78 subtree HM764102.1 9504 6 6 994.5 0.9774549 #> 80 79 subtree HM764317.1 9504 6 6 951.0 0.9584648 #> 81 80 subtree HM764901.1 9504 6 6 489.5 0.9824916 #> 82 81 subtree HM765175.1 9504 6 6 411.5 0.9233253 #> 83 82 subtree GQ279948.1 9504 3 5 464.0 0.7594512 #> 84 83 subtree HM762509.1 9504 5 5 521.0 0.9712644 #> 85 84 subtree HM764645.1 9504 5 5 674.0 0.9609467 #> 86 85 subtree HM764813.1 9504 5 5 573.0 0.9892734 #> 87 86 subtree FJ638414.1 9504 3 5 576.0 1.0000000 #> 88 87 subtree JQ933005.1 9504 1 5 878.0 0.9155983 #> 89 88 subtree JQ932259.1 9504 1 5 868.0 0.9529944 #> 90 89 subtree JQ932280.1 9504 4 5 554.0 0.7180095 #> 91 90 subtree JQ932662.1 9504 4 5 677.0 0.8219626 #> 92 91 subtree JQ932630.1 9504 1 5 843.0 0.8923251 #> 93 92 subtree JQ932880.1 9504 1 5 556.0 0.8463190 #> 94 93 subtree DQ989366.1 9504 5 5 428.0 0.9439252 #> 95 94 subtree FJ623078.1 9504 3 4 1374.0 1.0000000 #> 96 95 subtree DQ334827.1 9504 2 4 1196.5 0.7261749 #> 97 96 subtree AF042144.1/371..877 9504 2 4 507.0 0.9930966 #> 98 97 subtree AB181217.1/1545..1839 9504 4 4 296.5 0.5401961 #> 99 98 subtree AF397604.1/737..1037 9504 2 4 372.0 0.7777778 #> 100 99 subtree AY449010.1 9504 1 4 667.0 1.0000000 #> Definition Feature #> 1 aotus (0.07), partial (0.07) aovodrb (0.5), aonadrb (0.5) #> 2 aotus (0.09), class (0.09) mhcf (1) #> 3 antibody (0.05), construct (0.05) jp (0.3), kr (0.2) #> 4 aotus (0.2), genomic (0.2) - #> 5 gene (0.1), mitochondrial (0.1) coii (1) #> 6 allele (0.08), aotus (0.08) kir3ds3 (0.2), kir2ds5 (0.1) #> 7 dna (0.1), aotus (0.1) - #> 8 azarai (0.2), aotus (0.1) - #> 9 azarai (0.2), aotus (0.1) - #> 10 aotus (0.1), cytochrome (0.1) cytb (0.4), cytochrome (0.3) #> 11 aotus (0.08), cds (0.08) - #> 12 dna (0.2), aotus (0.1) - #> 13 aotus (0.2), genomic (0.2) - #> 14 aotus (0.08), cds (0.08) - #> 15 aotus (0.2), genomic (0.2) - #> 16 aotus (0.08), chain (0.08) - #> 17 aotus (0.2), genomic (0.2) - #> 18 alpha (0.09), aotus (0.09) rearrangement (0.5), vj (0.5) #> 19 aotus (0.09), cds (0.09) - #> 20 aotus (0.2), genomic (0.2) - #> 21 aotus (0.1), azarai (0.08) - #> 22 aotus (0.2), genomic (0.2) - #> 23 azarai (0.1), gene (0.08) - #> 24 aotus (0.2), genomic (0.2) - #> 25 sequence (0.2), aotus (0.1) - #> 26 aotus (0.2), genomic (0.2) - #> 27 aotus (0.08), beta (0.08) - #> 28 aotus (0.1), azarai (0.1) - #> 29 aotus (0.2), genomic (0.2) - #> 30 sry (0.2), aotus (0.1) sry (1) #> 31 aotus (0.1), sequence (0.1) - #> 32 aotus (0.08), cds (0.08) barcode (1) #> 33 aotus (0.1), clone (0.1) - #> 34 aotus (0.2), genomic (0.2) - #> 35 aotus (0.1), mrna (0.1) aotusb2m (0.5), b2m (0.5) #> 36 aotus (0.08), chain (0.08) - #> 37 aotus (0.1), gene (0.1) - #> 38 aotus (0.2), genomic (0.2) - #> 39 azarai (0.1), clone (0.1) - #> 40 aotus (0.09), chain (0.09) - #> 41 aotus (0.1), dennd5a (0.1) - #> 42 azarai (0.1), clone (0.1) - #> 43 aotus (0.08), azarai (0.08) - #> 44 aotus (0.1), cds (0.1) - #> 45 aotus (0.2), il2 (0.2) il2 (1) #> 46 aotus (0.1), cds (0.1) of (0.1), activity (0.07) #> 47 antigen (0.08), aotus (0.08) aonadqa1 (0.8), loc105708941 (0.2) #> 48 aotus (0.2), genomic (0.2) - #> 49 aotus (0.2), genomic (0.2) - #> 50 aotus (0.2), genomic (0.2) - #> 51 aotus (0.1), gene (0.1) - #> 52 aotus (0.1), gene (0.1) - #> 53 aotus (0.1), gene (0.1) - #> 54 aotus (0.1), gene (0.1) - #> 55 aotus (0.1), gene (0.1) - #> 56 aotus (0.1), gene (0.1) - #> 57 aotus (0.1), gene (0.1) - #> 58 aotus (0.1), gene (0.1) - #> 59 aotus (0.1), gene (0.1) - #> 60 aotus (0.1), gene (0.1) - #> 61 aotus (0.1), gene (0.1) - #> 62 aotus (0.1), gene (0.1) - #> 63 aotus (0.1), gene (0.1) - #> 64 aotus (0.1), gene (0.1) - #> 65 aotus (0.1), gene (0.1) - #> 66 aotus (0.1), gene (0.1) - #> 67 aotus (0.1), gene (0.1) - #> 68 aotus (0.1), gene (0.1) - #> 69 aotus (0.1), foxp1 (0.1) - #> 70 aotus (0.1), fes (0.1) - #> 71 aotus (0.1), fbn1 (0.1) - #> 72 aotus (0.1), fam123b (0.1) - #> 73 aotus (0.1), erc2 (0.1) - #> 74 aotus (0.1), edg1 (0.1) - #> 75 aotus (0.1), dctn2 (0.1) - #> 76 aotus (0.1), cnr1 (0.1) - #> 77 aotus (0.1), chrna1 (0.1) - #> 78 aotus (0.1), brca2 (0.1) - #> 79 aotus (0.1), bche (0.1) - #> 80 aotus (0.1), axin1 (0.1) - #> 81 aff2 (0.1), aotus (0.1) - #> 82 adora3 (0.1), aotus (0.1) - #> 83 aotus (0.2), genomic (0.2) - #> 84 aotus (0.1), dmrt1 (0.1) - #> 85 aotus (0.1), app (0.1) - #> 86 aff22 (0.1), aotus (0.1) - #> 87 aotus (0.1), bst2 (0.1) - #> 88 aotus (0.2), genomic (0.2) - #> 89 aotus (0.2), genomic (0.2) - #> 90 aotus (0.2), genomic (0.2) - #> 91 aotus (0.2), genomic (0.2) - #> 92 aotus (0.2), genomic (0.2) - #> 93 aotus (0.2), genomic (0.2) - #> 94 aotus (0.1), cds (0.1) ifngamma (1) #> 95 cd4 (0.2), aotus (0.1) - #> 96 gene (0.1), sequence (0.1) 16s (0.3), ribosomal (0.3) #> 97 aotus (0.1), mrna (0.1) aotusb2m (0.8), b2m (0.2) #> 98 aotus (0.09), gene (0.09) sinealu (0.4), color (0.2) #> 99 aotus (0.1), beta (0.08) loc105722736 (0.7), cgb (0.3) #> 100 autos (0.1), azarai (0.1) - #> [ reached getOption("max.print") -- omitted 93 rows ]
# the above generates a data.frame with information on each cluster: # ID - unique id in the object # Type - cluster type # Seed - most connected sequence # Parent - MRCA of all represented taxa # N_taxa - number of NCBI recognised taxa # N_seqs - number of sequences # Med_sql - median sequence length # MAD - Maximum alignment density, values close to 1 indicate all sequences in # the cluster have a similar length. # Definition - most common words (and frequency) in sequence definitions # Feature - most common feature name (and frequency)