adjustedCADD.annotation {Ravages}R Documentation

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)

[Package Ravages version 1.1.3 Index]