pctax
pctax provides a comprehensive suite of tools for
analyzing omics data.
Vignette
Please go to https://bookdown.org/Asa12138/pctax_book/ for the full vignette.
Install
Usage
It includes functionalities for α-diversity analysis, β-diversity analysis, differential abundance analysis, community assembly, visualization of phylogenetic tree and functional enrichment analysis…
Look at the test data:
library(pctax)
library(pcutils)
data(otutab, package = "pcutils")
# help(otutab)
head(otutab)
#> NS1 NS2 NS3 NS4 NS5 NS6 WS1 WS2 WS3 WS4
#> s__un_f__Thermomonosporaceae 1092 1920 810 1354 1064 1070 1252 1597 1330 941
#> s__Pelomonas_puraquae 1962 1234 2362 2236 2903 1829 644 495 1230 1284
#> s__Rhizobacter_bergeniae 588 458 889 901 1226 853 604 470 1070 1028
#> s__Flavobacterium_terrae 244 234 1810 673 1445 491 318 1926 1493 995
#> s__un_g__Rhizobacter 1432 412 533 759 1289 506 503 590 445 620
#> s__un_o__Burkholderiales 886 683 824 912 1502 1029 235 252 359 381
#> WS5 WS6 CS1 CS2 CS3 CS4 CS5 CS6
#> s__un_f__Thermomonosporaceae 1233 1011 2313 2518 1709 1975 1431 1527
#> s__Pelomonas_puraquae 953 635 1305 1516 844 1128 1483 1174
#> s__Rhizobacter_bergeniae 846 670 1029 1802 1002 1200 1194 762
#> s__Flavobacterium_terrae 577 359 1080 1218 754 423 1032 1412
#> s__un_g__Rhizobacter 657 429 1132 1447 550 583 1105 903
#> s__un_o__Burkholderiales 387 351 551 540 477 559 513 496
head(metadata)
#> Id Group env1 env2 env3 env4 env5 env6
#> NS1 NS1 NS 3.057248 10.23571 5.554576 8.084997 25.00795 -1.15456682
#> NS2 NS2 NS 4.830219 11.13453 5.613455 8.556829 16.67690 0.81168745
#> NS3 NS3 NS 3.753133 10.06232 5.582916 10.226572 21.68926 1.40733211
#> NS4 NS4 NS 4.262264 10.84401 5.258419 9.002256 24.81046 1.47805320
#> NS5 NS5 NS 2.476135 7.52584 6.255314 9.357587 19.70553 0.05813095
#> NS6 NS6 NS 5.131004 10.82761 5.180966 8.141506 18.39021 -1.70032569
#> lat long
#> NS1 26.94422 103.4767
#> NS2 29.08733 109.6196
#> NS3 28.25164 104.0361
#> NS4 33.82415 106.8651
#> NS5 33.51011 105.4571
#> NS6 31.86864 102.7832
head(taxonomy)
#> Kingdom Phylum
#> s__un_f__Thermomonosporaceae k__Bacteria p__Actinobacteria
#> s__Pelomonas_puraquae k__Bacteria p__Proteobacteria
#> s__Rhizobacter_bergeniae k__Bacteria p__Proteobacteria
#> s__Flavobacterium_terrae k__Bacteria p__Bacteroidetes
#> s__un_g__Rhizobacter k__Bacteria p__Proteobacteria
#> s__un_o__Burkholderiales k__Bacteria p__Proteobacteria
#> Class Order
#> s__un_f__Thermomonosporaceae c__Actinobacteria o__Actinomycetales
#> s__Pelomonas_puraquae c__Betaproteobacteria o__Burkholderiales
#> s__Rhizobacter_bergeniae c__Gammaproteobacteria o__Pseudomonadales
#> s__Flavobacterium_terrae c__Flavobacteriia o__Flavobacteriales
#> s__un_g__Rhizobacter c__Gammaproteobacteria o__Pseudomonadales
#> s__un_o__Burkholderiales c__Betaproteobacteria o__Burkholderiales
#> Family
#> s__un_f__Thermomonosporaceae f__Thermomonosporaceae
#> s__Pelomonas_puraquae f__Comamonadaceae
#> s__Rhizobacter_bergeniae f__Pseudomonadaceae
#> s__Flavobacterium_terrae f__Flavobacteriaceae
#> s__un_g__Rhizobacter f__Pseudomonadaceae
#> s__un_o__Burkholderiales f__un_o__Burkholderiales
#> Genus
#> s__un_f__Thermomonosporaceae g__un_f__Thermomonosporaceae
#> s__Pelomonas_puraquae g__Pelomonas
#> s__Rhizobacter_bergeniae g__Rhizobacter
#> s__Flavobacterium_terrae g__Flavobacterium
#> s__un_g__Rhizobacter g__Rhizobacter
#> s__un_o__Burkholderiales g__un_o__Burkholderiales
#> Species
#> s__un_f__Thermomonosporaceae s__un_f__Thermomonosporaceae
#> s__Pelomonas_puraquae s__Pelomonas_puraquae
#> s__Rhizobacter_bergeniae s__Rhizobacter_bergeniae
#> s__Flavobacterium_terrae s__Flavobacterium_terrae
#> s__un_g__Rhizobacter s__un_g__Rhizobacter
#> s__un_o__Burkholderiales s__un_o__BurkholderialesCitation
Please cite:
Chen Peng (2023). pctax: Professional Comprehensive Omics Data Analysis. R package, https://github.com/Asa12138/pctax.