read_finalreport_snps: Read Illumina array raw data

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

Description

read_finalreport handles inputs of data in FinalReport-like format

Usage

read_finalreport_snps(
  DT_path,
  mark_ID_col = "SNP Name",
  chr_col = "Chr",
  pos_col = "Position"
)

Arguments

DT_path,	path to the input file.
mark_ID_col,	name of the column containing the SNP ID information in the input file. Default is "SNP Name".
chr_col,	name of the column containing the chromosome information in the input file. Default is "Chr".
pos_col,	name of the column containing the SNPs position information in the input file. Default is "Position".

Details

This function is used to load data in FinalReport like format into a data.table containing the SNPs markers information (i.e. chromosome and position). The function expect a single file where each markers is present one single time. Similar files are often required or produced by the calling algorithm/pipeline, e.g. the PFB file in PennCNV can be used here.

Value

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

Examples

DT <- read_finalreport_snps(system.file("extdata", "SNP.pfb", package = "CNVgears"),
mark_ID_col = "Name", chr_col = "Chr", pos_col = "Position")

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