read_NGS_raw: Read raw copyratio/LRR data for NGS intervals

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

Description

read_NGS_raw

Usage

read_NGS_raw(
  DT_path,
  rds_path,
  pref,
  suff,
  chr_col,
  start_col,
  end_col,
  raw_col,
  raw_type,
  sample_list,
  markers
)

Arguments

DT_path,	path to the input file.
rds_path,	path to the directory where RDS should be stored.
pref, suff,	eventual prefix an suffix (e.g. ".txt"). If not necessary must be set to NA.
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.
raw_col,	name of the column containing the marker-level raw data in the input file.
raw_type,	character, it describes the format in which the LRR-like data is give. Can be either "log2R", "numeric_CN" or "copyratio", see description.
sample_list,	a data.table, the output of read_metadt.
markers,	a data.table, the output of read_NGS_intervals or read_finalreport_snps, depending on the initial data type.

Details

This function handles the input, pre-processing and temporary storage (as RDS files) of the the markers-level raw data for each sample. Those are mostly required for CNVs inheritance detection. Any marker-level log2R-like measure is supported, given that, for somatic chromosomes: $$LRR = log2R = log2(CopyRatio) = log2(numeric_CN/2*)$$ Input must be one file per sample.

Value

nothing, this function saves the results on disk.

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