readDesign: Read design file

In acc-bioinfo/TMBleR: Tumor Mutational Burden Quantification From Gene Panels And WES

Description

Read the file describing the design of the sequencing experiment (i.e. the targeted regions in the sequencing experiment). It can be either a BED file containing genomic coordinates of the targeted genes or a TXT file containing symbols for targeted genes.

Usage

readDesign(filename, assembly, ids, name = NULL)

Arguments

filename	name of file describing the sequencing design. It requires ".bed" extension for files containing the genomic coordinates of the targeted regions or ".txt" extension for files containing the gene symbol of targeted genes. BED files must be tab-delimited, with no track description line and it must report at least CHR START and END information.
assembly	human genome assembly: hg19 or hg38
ids	type of gene identifiers, if .txt file with gene list is provided: hgnc_symbol or entrezgene_id.
name	string indicating the name of the design. if not specified, the filename without extension will be used instead.

Value

data.frame with genomic coordinates or a character vector with symbols of targeted genes

Author(s)

Laura Fancello

Examples

#Read in input the panel sequencing design (either a BED file with genomic
#coordinates of the targeted genes or TXT file with targeted gene names).
design_FromTxt <- readDesign(filename = system.file("extdata",
                                 "ExamplePanel_GeneIDs.txt",
                                 package = "TMBleR",
                                 mustWork = TRUE),
                     assembly = "hg19",
                     ids = "entrezgene_id")

design_FromBed <- readDesign(filename = system.file("extdata",
                                "ExamplePaneldesign.bed",
                                 package = "TMBleR",
                                 mustWork = TRUE),
                              assembly = "hg19")

acc-bioinfo/TMBleR documentation built on Dec. 18, 2021, 10:21 p.m.