sortScoredVariants: Sorts variants by the number of score cutoffs passed

Description Usage Arguments Value Author(s) Examples

Description

Takes annotated variants with scores, compares the scores of each variant to score cutoffs, and organizes variants based on how variant scores are passed.

Usage

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sortScoredVariants(df, cadd.min = 20, fitCon.min = 0.4, phastCon.min = 0.55, mcap.min = 0.025, AFgnomAD.max = 0.01, sift.max = 0.05, polyphen.min = 0.909)

Arguments

df

Annoted variant dataframe.

cadd.min

Minimum CADD score accepted

fitCon.min

Minimum fitCon score accepted

phastCon.min

Minimum phastCon score accepted

mcap.min

Minimum M-CAP score accepted

AFgnomAD.max

Maximum gnomAD Allele Frequency accepted

sift.max

Maximum SIFT score accepted

polyphen.min

Miniumum PolyPhen accepted

Value

A data frame of variants sorted by the number of variant scores passed.

Author(s)

Kate Sanders

Examples

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##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.


data("MUC1_variants")
cleanVariants <- removeUnwantedVariants(MUC1_variants)
annotatedVariants <- addVariantAnnotations(cleanVariants, "MUC1")
scoreSortedVariants <- sortScoredVariants(annotatedVariants)

SandersKM/MendelianVariants documentation built on May 12, 2019, 4:35 a.m.