Mercurial > repos > rnateam > nastiseq
view test-data/test.r @ 0:0a0bba8e1823 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq commit 8b472e8680bb0ae5d11ee48b642ab305f9333a48
author | rnateam |
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date | Wed, 22 Feb 2017 07:32:08 -0500 |
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library(NASTIseq) ## generation of test set # data(WholeRoot) # WholeRoot$genepos$feature <- 'gene' # # set_attri <- function(attri){ # attri = paste('gene_id ', '"', attri, '"', ';', sep = '') # return(attri) # } # # WholeRoot$genepos$attributes = as.character(lapply(as.character(WholeRoot$genepos$attributes), set_attri)) # # write.table(WholeRoot$genepos, file = "input_TAIR10_annotation.gtf", row.names = FALSE, col.names = FALSE, sep = "\t", quote = FALSE) # write.table(WholeRoot$smat, file = "input_read_count_smt.tsv", col.names = FALSE, sep = "\t", quote = FALSE) # write.table(WholeRoot$asmat, file = "input_read_count_asmt.tsv", col.names = FALSE, sep = "\t", quote = FALSE) # # write.table(WholeRoot$pospairs, file = "input_positive_pair.tsv", row.names = FALSE, col.names = FALSE, sep = "\t", quote = FALSE) genepos = read.delim("input_TAIR10_annotation.gtf", header=FALSE, comment.char="#") colnames(genepos) = c("seqname", "source", "feature", "start", "end", "score", "strand", "frame", "attributes") genepos = subset(genepos, feature=="gene") get_id = function(attri){ gene_info = strsplit(attri, ";")[[1]][1] gene_id = strsplit(gene_info, " ")[[1]][2] gene_id = gsub("\"", "", gene_id) return(gene_id) } genepos$attributes = as.character(lapply(as.character(genepos$attributes), get_id)) pospairs = read.table("input_positive_pair.tsv", sep = "\t", as.is = TRUE) smat = as.matrix(read.table("input_read_count_smt.tsv", sep = "\t", row.names = 1)) asmat = as.matrix(read.table("input_read_count_asmt.tsv", sep = "\t", row.names = 1)) WRscore = getNASTIscore(smat, asmat) negpairs = getnegativepairs(genepos) WRpred = NASTIpredict(smat,asmat, pospairs, negpairs) WRpred_rocr = prediction(WRpred$predictions,WRpred$labels) thr = defineFDR(WRpred_rocr,0.05) WR_names = FindNATs(WRscore, thr, pospairs, genepos) write.table(WR_names$newpairs, file = "output_newpairs.tsv", row.names = FALSE, col.names = FALSE, sep = "\t", quote = FALSE) write.table(WR_names$neworphan, file = "output_neworphan.tsv", row.names = FALSE, col.names = FALSE, sep = "\t", quote = FALSE)