buildInput: Build input file

In Manuelaio/uncoverappLib: Interactive graphical application for clinical assessment of sequence coverage at the base-pair level

Build input file

Description

Function to build input file for unCOVERAPP when the number of genes to analyze is > 50.

Usage

buildInput(
  geneList,
  genome,
  type_bam,
  bamList,
  outDir,
  type_input,
  MAPQ.min = 1,
  base.quality = 1
)

Arguments

geneList	a text file, named with .txt extension, containing HGNC official gene name(s) one per row.
genome	(char) reference genome, hg19 or hg38
type_bam	(char) chromosome notation of their BAM file(s). Use "number" or "chr". In the BAM file, the number option refers to 1, 2, ..., X,.M chromosome notation, while the chr option refers to chr1, chr2, ... chrX, chrM chromosome notation.
bamList	a text file, named with .list extension, containing the absolute paths to BAM file(s) one per row.
outDir	(char) directory where pileup output will be stored
type_input	(char) type of input target. Use "target" or "genes". If you use a list of gene names use "genes", if you use a target bed use "target".
MAPQ.min	(integer) minimum MAPQ value for an alignment to be included in output file.
base.quality	(integer) minimum QUAL value for each nucleotide in an alignment.

Value

Two file: a file.bed containing tab-separated specifications of genomic coordinates (chromosome, start position, end position), the coverage value, and the reference:alternate allele counts for each position and a file.txt with statistical summary of coverage

Examples

gene.list<- system.file("extdata", "mygene.txt", package = "uncoverappLib")

bam_example <- system.file("extdata", "example_POLG.bam",
package = "uncoverappLib")
cat(bam_example, file = "bam.list", sep = "\n")
temp_dir=tempdir()
buildInput(geneList= gene.list, genome= "hg19", type_bam= "chr",
bamList= "bam.list",type_input="genes", outDir= temp_dir)

Manuelaio/uncoverappLib documentation built on Feb. 16, 2023, 12:52 a.m.