read_finalreport_raw: 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_raw(
  DT_path,
  rds_path,
  pref,
  suff,
  sample_list,
  markers,
  chr_col = "Chr",
  pos_col = "Position",
  LRR_col = "Log R Ratio",
  BAF_col = "B Allele Freq"
)

Arguments

DT_path,	character, the path to the directory with the raw data (i.e. the splitted final reports)
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.
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.
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".
LRR_col,	name of the column containing the LRR information in the input file. Default is "Log R Ratio".
BAF_col,	name of the column containing the BAF information in the input file. Default is "B Allele Freq".

Details

This function handles the input, pre-processing and temporary storage (as RDS files) of the the markers-level raw data for each sample starting from FinalReport-like files (any plain text file with columns header can be read). Input must be one file per sample.

Value

nothing, this function saves the results on disk.

Examples

read_finalreport_raw(DT_path = system.file("extdata", package = "CNVgears"),
                    pref = "Final_report_example", suff = ".txt",
                    rds_path = file.path("tmp_RDS"),
                    markers = markers_examples,
                    sample_list = cohort_examples[sample_ID == "NA12878", ])

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