Outputproseq {customProDB} | R Documentation |
Get the FASTA file of proteins that pass RPKM cutoff. the FASTA ID line contains protein ID, gene ID, HGNC symbol and description
Outputproseq(rpkm, cutoff = "30%", proteinseq, outfile, ids, ...)
rpkm |
a numeric vector containing RPKM for each protein |
cutoff |
cutoff of RPKM value. Two options are available, percentage format or RPKM. By default we use "30 proteins according to their RPKMs. |
proteinseq |
a dataframe containing protein ids and protein sequences. |
outfile |
output file name. |
ids |
a dataframe containing gene/transcript/protein id mapping information. |
... |
additional arguments |
by taking the RPKM value as input, the function outputs sequences of the proteins that pass the cutoff.
FASTA file contains proteins with RPKM above the cutoff.
Xiaojing Wang
load(system.file("extdata/refseq", "exon_anno.RData", package="customProDB")) load(system.file("extdata/refseq", "proseq.RData", package="customProDB")) bamFile <- system.file("extdata/bams", "test1_sort.bam", package="customProDB") load(system.file("extdata/refseq", "ids.RData", package="customProDB")) RPKM <- calculateRPKM(bamFile, exon, proteincodingonly=TRUE, ids) outf1 <- paste(tempdir(), '/test_rpkm.fasta', sep='') Outputproseq(RPKM, 1, proteinseq, outf1, ids)