adjustedCADD_annotation: SNVs and Indels annotation with adjusted CADD scores

In genostats/Ravages: Rare Variant Analysis and Genetic Simulations

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 with the columns 'chr', 'pos', 'A1', 'A2' and 'adjCADD' 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 with the columns 'chr', 'pos', 'A1', 'A2' and 'PHRED_1.4' 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

bedtools need to be installed on the system to run this function if indels are present are if scores are not provided for SNVs.

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)

genostats/Ravages documentation built on Oct. 11, 2023, 11:10 p.m.