adjustedCADD.annotation.SNVs {Ravages} | R Documentation |
SNVs annotation with adjusted CADD scores
Description
Annotate SNVs with the adjusted CADD scores (CADD PHRED scores for coding, regulatory and intergenic regions)
Usage
adjustedCADD.annotation.SNVs(x, variant.scores = NULL,
cores = 10, verbose = T, path.data)
Arguments
x |
A bed.matrix annotated with CADD regions using |
variant.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) |
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
SNVs are directly annotated with the adjusted CADD scores in the function using the file "AdjustedCADD_v1.4_202108.tsv.gz" downloaded from https://lysine.univ-brest.fr/RAVA-FIRST/ in the repository of the package Ravages or the scores of variants can be provided to variant.scores
to gain in computation time (this file should contain 5 columns: the chromosome ('chr'), position ('pos'), reference allele ('A1'), alternative allele ('A2') and adjusted CADD scores ('adjCADD').
Those adjusted scores are used in the RAVA.FIRST()
pipeline to filter rare variants.
As this function can take time when a large number of SNVs are present, it is recommended to use this function chromosome by chromosome for large datasets or to fitler the bed matrix before the annotation.
Value
The bed matrix x with adjusted CADD scores in adjCADD
.
Source
https://lysine.univ-brest.fr/RAVA-FIRST/
See Also
adjustedCADD.annotation, 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.SNVs(x)