adjustedCADD.annotation | R Documentation |
Annotate SNVs and Indels with the adjusted CADD scores (CADD PHRED scores for coding, regulatory and intergenic regions)
adjustedCADD.annotation(x, SNVs.scores = NULL, indels.scores = NULL,
cores = 10, verbose = T, path.data)
x |
A bed.matrix annotated with CADD regions using |
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 |
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/ |
This function calls adjustedCADD.annotation.SNVs
and adjustedCADD.annotation.indels
. See the help of those two functions for more details.
The bed matrix x with adjusted CADD scores in adjCADD
.
https://lysine.univ-brest.fr/RAVA-FIRST/
adjustedCADD.annotation.SNVs, adjustedCADD.annotation.indels, RAVA.FIRST
, filter.adjustedCADD
#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)
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