VariantFiltering-deprecated: Deprecated functions in package 'VariantFiltering'

In VariantFiltering: Filtering of coding and non-coding genetic variants

Description

These functions are provided for compatibility with older versions of ‘VariantFiltering’ only, and will be defunct at the next release.

Details

The following functions are deprecated and will be made defunct; use the replacement indicated below:

• dbSNPpresent(): This functionality is now replaced by the combined used of functions filters(), active(), cutoffs(), codechange()

• OMIMpresent(): This functionality is now replaced by the combined used of functions filters(), active(), cutoffs(), codechange()

• variantType(): This functionality is now replaced by the combined used of functions filters(), active(), cutoffs(), codechange()

• aaChangeType(): This functionality is now replaced by the combined used of functions filters(), active(), cutoffs(), codechange()

• variantLocation(): This functionality is now replaced by the combined used of functions filters(), active(), cutoffs(), codechange()

• variantConsequence(): This functionality is now replaced by the combined used of functions filters(), active(), cutoffs(), codechange()

• naMAF(): This functionality is now replaced by the combined used of functions filters(), active(), cutoffs(), codechange()

• MAFpop(): This functionality is now replaced by the combined used of functions filters(), active(), cutoffs(), codechange()

• maxMAF(): This functionality is now replaced by the combined used of functions filters(), active(), cutoffs(), codechange()

• minPhastCons(): This functionality is now replaced by the combined used of functions filters(), active(), cutoffs(), codechange()

• minPhylostratum(): This functionality is now replaced by the combined used of functions filters(), active(), cutoffs(), codechange()

• minScore5ss(): This functionality is now replaced by the combined used of functions filters(), active(), cutoffs(), codechange()

• minScore3ss(): This functionality is now replaced by the combined used of functions filters(), active(), cutoffs(), codechange()

• minCUfc(): This functionality is now replaced by the combined used of functions filters(), active(), cutoffs(), codechange()

Author(s)

Robert Castelo <[e-mail]>

VariantFiltering documentation built on Nov. 8, 2020, 7:25 p.m.