Description Usage Arguments Value Author(s) Examples
Takes annotated variants with scores, compares the scores of each variant to score cutoffs, and organizes variants based on how variant scores are passed.
1 | 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)
|
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 |
A data frame of variants sorted by the number of variant scores passed.
Kate Sanders
1 2 3 4 5 6 7 8 9 | ##---- 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)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.