read_finalreport_snps {CNVgears} | R Documentation |
read_finalreport
handles inputs of data in FinalReport-like format
read_finalreport_snps( DT_path, mark_ID_col = "SNP Name", chr_col = "Chr", pos_col = "Position" )
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 |
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 |
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.
a data.table
, will be of Markers
class in future
versions.
DT <- read_finalreport_snps(system.file("extdata", "SNP.pfb", package = "CNVgears"), mark_ID_col = "Name", chr_col = "Chr", pos_col = "Position")