read_NGS_raw {CNVgears} | R Documentation |
read_NGS_raw
read_NGS_raw( DT_path, rds_path, pref, suff, chr_col, start_col, end_col, raw_col, raw_type, sample_list, markers )
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 |
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 |
markers, |
a |
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.
nothing, this function saves the results on disk.