merge_calls {CNVgears} | R Documentation |
merge_calls
screen the segments of a sample and merge adjacent calls
with equal GT if close enough
merge_calls(DT_in, prop = 0.3)
DT_in |
a |
prop |
numeric value that multiplied by the length of a call gives the range where adjacent calls are searched. |
This function takes a CVNResults
object and try to merge adjacent calls
(having equal GT and being close
enough). It is designed to process one sample at the time and is integrated
in the function read_results
. It is not suggested to use it
stand-alone. The merging is done starting from the larger calls, on adjacent
call with equal GT in a range of +/- length*prop
, trough several
iterations until no more calls can be merged.
a CNVresults
, DT_in
processing result.
# with merge DT <- read_results(DT_path = system.file("extdata", "chrs_14_22_cnvs_penn.txt", package = "CNVgears"), res_type = "file", DT_type = "TSV/CSV", chr_col = "chr", start_col = "posStart", end_col = "posEnd", CN_col = "CN", samp_ID_col = "Sample_ID", sample_list = cohort_examples, markers = markers_examples, method_ID = "P") # without DT <- read_results(do_merge = FALSE, DT_path = system.file("extdata", "chrs_14_22_cnvs_penn.txt", package = "CNVgears"), res_type = "file", DT_type = "TSV/CSV", chr_col = "chr", start_col = "posStart", end_col = "posEnd", CN_col = "CN", samp_ID_col = "Sample_ID", sample_list = cohort_examples, markers = markers_examples, method_ID = "P")