| Title: | Generating SAM file for PSMs in shotgun proteomics data |
|---|---|
| Description: | Mapping PSMs back to genome. The package builds SAM file from shotgun proteomics data The package also provides function to prepare annotation from GTF file. |
| Authors: | Xiaojing Wang |
| Maintainer: | Xiaojing Wang <[email protected]> |
| License: | Artistic-2.0 |
| Version: | 1.41.0 |
| Built: | 2024-10-31 03:38:17 UTC |
| Source: | https://github.com/bioc/proBAMr |
prepare the annotation from GENCODE. Download GTF and FASTA files from GENCODE ftp first. Read introduction for more information.
PrepareAnnotationGENCODE(gtfFile, CDSfasta, pepfasta, annotation_path, dbsnp = NULL, splice_matrix = FALSE, COSMIC = FALSE, ...)PrepareAnnotationGENCODE(gtfFile, CDSfasta, pepfasta, annotation_path, dbsnp = NULL, splice_matrix = FALSE, COSMIC = FALSE, ...)
gtfFile |
specify GTF file location. |
CDSfasta |
path to the fasta file of coding sequence. |
pepfasta |
path to the fasta file of protein sequence. |
annotation_path |
specify a folder to store all the annotations. |
dbsnp |
specify a snp dataset to be used for the SNP annotation, default is NULL. (e.g. "snp135") |
splice_matrix |
whether generate a known exon splice matrix from the annotation. this is not necessary if you don't want to analyse junction results, default is FALSE. |
COSMIC |
whether to download COSMIC data, default is FALSE. |
... |
additional arguments |
several .RData files containing annotations needed for further analysis.
Xiaojing Wang
gtfFile <- system.file("extdata", "test.gtf", package="proBAMr") CDSfasta <- system.file("extdata", "coding_seq.fasta", package="proBAMr") pepfasta <- system.file("extdata", "pro_seq.fasta", package="proBAMr") annotation_path <- tempdir() PrepareAnnotationGENCODE(gtfFile, CDSfasta, pepfasta, annotation_path, dbsnp=NULL, splice_matrix=FALSE, COSMIC=FALSE)gtfFile <- system.file("extdata", "test.gtf", package="proBAMr") CDSfasta <- system.file("extdata", "coding_seq.fasta", package="proBAMr") pepfasta <- system.file("extdata", "pro_seq.fasta", package="proBAMr") annotation_path <- tempdir() PrepareAnnotationGENCODE(gtfFile, CDSfasta, pepfasta, annotation_path, dbsnp=NULL, splice_matrix=FALSE, COSMIC=FALSE)
Generate SAM files from confident peptide-spectrum-matches (PSMs).
PSMtab2SAM(passedPSM, XScolumn = "mvh", exon_anno, proteinseq, procodingseq, ...)PSMtab2SAM(passedPSM, XScolumn = "mvh", exon_anno, proteinseq, procodingseq, ...)
passedPSM |
a data frame of PSMs passed FDR. |
XScolumn |
specify the column which represents the matching score. |
exon_anno |
a dataframe of exon annotations. |
proteinseq |
a dataframe containing protein ids and protein sequences. |
procodingseq |
a data frame cotaining coding sequence for each protein. |
... |
additional arguments |
a dataframe containing
Xiaojing Wang
load(system.file("extdata/GENCODE", "exon_anno.RData", package="proBAMr")) load(system.file("extdata/GENCODE", "proseq.RData", package="proBAMr")) load(system.file("extdata/GENCODE", "procodingseq.RData", package="proBAMr")) options(stringsAsFactors=FALSE) passedPSM <- read.table(system.file("extdata", "passedPSM.tab", package="proBAMr"), sep='\t', header=TRUE) SAM <- PSMtab2SAM(passedPSM, XScolumn='mvh', exon, proteinseq, procodingseq) write.table(SAM, file=paste(tempdir(), '/test.sam', sep=''), sep='\t', quote=FALSE, row.names=FALSE, col.names=FALSE)load(system.file("extdata/GENCODE", "exon_anno.RData", package="proBAMr")) load(system.file("extdata/GENCODE", "proseq.RData", package="proBAMr")) load(system.file("extdata/GENCODE", "procodingseq.RData", package="proBAMr")) options(stringsAsFactors=FALSE) passedPSM <- read.table(system.file("extdata", "passedPSM.tab", package="proBAMr"), sep='\t', header=TRUE) SAM <- PSMtab2SAM(passedPSM, XScolumn='mvh', exon, proteinseq, procodingseq) write.table(SAM, file=paste(tempdir(), '/test.sam', sep=''), sep='\t', quote=FALSE, row.names=FALSE, col.names=FALSE)