read_finalreport_raw {CNVgears} | R Documentation |
read_finalreport
handles inputs of data in FinalReport-like format
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" )
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 |
sample_list, |
a |
markers, |
a |
chr_col, |
name of the column containing the chromosome information in
the input file. Default is |
pos_col, |
name of the column containing the SNPs position information
in the input file. Default is |
LRR_col, |
name of the column containing the LRR information in the
input file. Default is |
BAF_col, |
name of the column containing the BAF information in the
input file. Default is |
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.
nothing, this function saves the results on disk.
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", ])