sample2experiment.Rd
This function generates counts, FPKM and TPM tables from rnaseqCounts outuputs.
sample2experiment( sample.folders, covariates, batch = NULL, bio.type = c("protein_coding", "unitary_pseudogene", "unprocessed_pseudogene", "processed_pseudogene", "transcribed_unprocessed_pseudogene", "processed_transcript", "antisense", "transcribed_unitary_pseudogene", "polymorphic_pseudogene", "lincRNA", "sense_intronic", "transcribed_processed_pseudogene", "sense_overlapping", "IG_V_pseudogene", "pseudogene", "TR_V_gene", "3prime_overlapping_ncRNA", "IG_V_gene", "bidirectional_promoter_lncRNA", "snRNA", "miRNA", "misc_RNA", "snoRNA", "rRNA", "IG_C_gene", "IG_J_gene", "TR_J_gene", "TR_C_gene", "TR_V_pseudogene", "TR_J_pseudogene", "IG_D_gene", "ribozyme", "IG_C_pseudogene", "TR_D_gene", "TEC", "IG_J_pseudogene", "scRNA", "scaRNA", "vaultRNA", "sRNA", "macro_lncRNA", "non_coding", "IG_pseudogene"), output.prefix = "." )
sample.folders, | a character string indicating the paths of rnaseqCouts output folders |
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covariates, | a character string indicating the covariates associated to each sample. Covariates are required for differnetial expression analysis |
batch, | a character string indicating the batch associated to each sample |
bio.type, | a character string indicating the ensemb bio.type. Options: "protein_coding","unitary_pseudogene","unprocessed_pseudogene","processed_pseudogene", "transcribed_unprocessed_pseudogene","processed_transcript","antisense","transcribed_unitary_pseudogene","polymorphic_pseudogene","lincRNA","sense_intronic","transcribed_processed_pseudogene","sense_overlapping","IG_V_pseudogene","pseudogene","TR_V_gene","3prime_overlapping_ncRNA","IG_V_gene","bidirectional_promoter_lncRNA","snRNA","miRNA","misc_RNA","snoRNA","rRNA","IG_C_gene","IG_J_gene","TR_J_gene","TR_C_gene","TR_V_pseudogene","TR_J_pseudogene","IG_D_gene","ribozyme","IG_C_pseudogene","TR_D_gene","TEC","IG_J_pseudogene","scRNA","scaRNA","vaultRNA","sRNA","macro_lncRNA","non_coding","IG_pseudogene" |
output.prefix, | a character value indicating the output folder path |
Returns counts, fpkm, tpm data frames for gene and isoforms, save data frames in experiment.tables.Rda, in counts.txt, log2fpkm.txt and in log2TPM
if (FALSE) { system("wget http://130.192.119.59/public/test.samples2experiment.zip") unzip("test.samples2experiment.zip") setwd("test.samples2experiment") library(docker4seq) sample2experiment(sample.folders=c("./e1g","./e2g","./e3g", "./p1g", "./p2g", "./p3g"), covariates=c("Cov.1","Cov.1","Cov.1", "Cov.2","Cov.2","Cov.2"), bio.type="protein_coding", output.prefix=".") }