transcriptInfoFile: Manage file containing information about transcript reference

In BitSeq: Transcript expression inference and differential expression analysis for RNA-seq data

Description

Manage file containing information about the transcript reference. These functions are used for verifying and updating transcript information DataFrame.

Usage

tri.file.hasGeneNames(trInfoFile)
tri.file.setGeneNames(trInfoFile, geneNames, transcriptNames=NULL)

Arguments

trInfoFile	Name of the file containing transcript information or the where the information should be stored.
geneNames	Vector with new gene names that should be assigned to transcripts.
transcriptNames	Names of transcripts that should be associated with the gene names.

Details

If not provided with the information, BitSeq extracts information about the transcript reference from the alignment and sequence files. This information is stored in so called transcript information(trInfo) file, usually having extension .tr. This file contains columns with gene names (if available), transcript names, transcript lengths and optionally with adjusted lengths of transcripts. Important use of trInfo file is for calculating gene expression or within gene expression, where the file is used for determining which transcripts belong to which genes. However, for this the gene names have to be properly set in the transcript info, which is not always the case.

Function tri.file.hasGeneNames determines whether gene names are properly set in the transcript information file and returns TRUE or FALSE and a warning message identifying the problem.

Function tri.file.setGeneNames updates the gene names of a transcript information in file provided by argument trInfoFile. The vector geneNames should provide gene names of transcripts and be of the same length as is the number of transcripts. The gene names have to be either ordered as their appropriate transcripts in trInfoFile file, or if ordered differently, vector of transcript names, ordered as gene names has to be provided by argument transcriptNames. The names in transcriptNames have to correspond to the transcript names in actual file.

Value

Function tri.file.hasGeneNames returns boolean value.

Author(s)

Peter Glaus

See Also

getExpression, getGeneExpression, tri.load, tri.save

Examples

setwd(system.file("extdata",package="BitSeq"))
## this should be true
tri.file.hasGeneNames("ensSelect1.tr")

BitSeq documentation built on Nov. 8, 2020, 5:25 p.m.