adjustedCADD.annotation {Ravages}

SNVs and Indels annotation with adjusted CADD scores

Description

Annotate SNVs and Indels with the adjusted CADD scores (CADD PHRED scores for coding, regulatory and intergenic regions)

Usage

adjustedCADD.annotation(x, SNVs.scores = NULL, indels.scores = NULL,
			cores = 10, verbose = T, path.data)

Arguments

x

A bed.matrix annotated with CADD regions using set.CADDregions

SNVs.scores

A dataframe containing the ADJUSTED CADD scores of the SNVs (Optional, useful to gain in computation time if the adjusted CADD scores of variants in the study are available)

indels.scores

A dataframe containing the CADD PHREDv1.4 scores of the indels - Compulsory if indels are present in x

cores

How many cores to use, set at 10 by default

verbose

Whether to display information about the function actions

path.data

The repository where data for RAVA-FIRST are or will be downloaded from https://lysine.univ-brest.fr/RAVA-FIRST/

Details

This function calls adjustedCADD.annotation.SNVs and adjustedCADD.annotation.indels. See the help of those two functions for more details.

Value

The bed matrix x with adjusted CADD scores in adjCADD.

Source

https://lysine.univ-brest.fr/RAVA-FIRST/

See Also

adjustedCADD.annotation.SNVs, adjustedCADD.annotation.indels, RAVA.FIRST, filter.adjustedCADD

Examples

#Import 1000Genome data from region around LCT gene
#x <- as.bed.matrix(LCT.gen, LCT.fam, LCT.bim)

#Annotate variants with adjusted CADD score
#x <- adjustedCADD.annotation(x)