mkMutProfileSnvIndel: Create annotations to the germline/somatic tables originating...
In luannnguyen/hmfGeneAnnotation: Determines gene amplifications and biallelic losses from HMF pipeline output
Description
Usage
Arguments
Value
Description
Primarily used to determine
Usage
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mkMutProfileSnvIndel(
df.snv.indel,
scoring = SCORING_MUT,
keep.only.first.eff = T,
filter.no.impact.variants = T,
verbose = T
)
Arguments
df.snv.indel
A germline/somatic table originating from HMF germline/somatic vcfs
scoring
A list containing the scoring for snpeff, clinvar, and enigma annotation values
keep.only.first.eff
Only keep first snpeff_eff (items are separated by '&')?
verbose
Show messages?
Value
The original input dataframe with annotation columns
luannnguyen/hmfGeneAnnotation documentation built on May 6, 2020, 1:07 p.m.
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Description Usage Arguments Value
Description
Primarily used to determine
Usage
1 2 3 4 5 6 7 | mkMutProfileSnvIndel(
df.snv.indel,
scoring = SCORING_MUT,
keep.only.first.eff = T,
filter.no.impact.variants = T,
verbose = T
)
|
Arguments
df.snv.indel |
A germline/somatic table originating from HMF germline/somatic vcfs |
scoring |
A list containing the scoring for snpeff, clinvar, and enigma annotation values |
keep.only.first.eff |
Only keep first snpeff_eff (items are separated by '&')? |
verbose |
Show messages? |
Value
The original input dataframe with annotation columns
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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