Filter the Called snp array

Source: R/filter_called.R

Filter the Called snp array

filter_called(
  called,
  DP_min = 5,
  DP_max = 80,
  ref_call = 1,
  alt_call = 1,
  overlaps = 1,
  min_VDB = 0.1
)

Arguments

called

CollapsedVCF containing filtered snp info for rna data
DP_min

TODO
DP_max

TODO
ref_call

TODO
alt_call

TODO
overlaps

TODO
min_VDB

TODO

Value

Filtered snp array

Examples

dim(snpsCalled_VCF)
#> [1] 665  42
snpsCalled_filter <- filter_called(snpsCalled_VCF)
dim(snpsCalled_filter)
#> [1] 255  42