read_NGS_intervals: Read genomic intervals

In SinomeM/CNVgears: A Framework to Combine, Analize and Interpret CNVs Calling Results

Description

read_intervals handles inputs of data used as the markers in CNVs calling/segmentation using NGS data (WES or WGS)

Usage

read_NGS_intervals(
  DT_path,
  chr_col = "CONTIG",
  start_col = "START",
  end_col = "END"
)

Arguments

DT_path,	path to the input file.
chr_col,	name of the column containing the chromosome information in the input file.
start_col,	name of the column containing the start information in the input file.
end_col,	name of the column containing the end information in the input file.

Details

This function is used to load data in interval list or BED like formats into a data.table that integrates with the other functions of the package. This is usually done at the beginning of a project involving CNVs calling/segmentation on NGS data (WES or WGS) pipelines' results analysis. The function should automatically skip any eventual header. The parameters default values are for file in GATK interval list like format.

Value

a data.table, will be of Markers class in future versions.

Examples

read_NGS_intervals(DT_path = system.file("extdata", "markers_WES_example.tsv",
package = "CNVgears"), chr_col = "chr", start_col = "start", end_col = "end")

SinomeM/CNVgears documentation built on Nov. 21, 2021, 5:34 a.m.