Assign functional prediction rfPred scores to human missense variants

Description

rfPred is a statistical method which combines 5 algorithms predictions in a random forest model: SIFT, Polyphen2, LRT, PhyloP and MutationTaster. These scores are available in the dbNFSP database for all the possible missense variants in hg19 version, and the package rfPred gives a composite score more reliable than each of the isolated algorithms.

Arguments

Value

The variants list with the assigned rfPred scores, as well as the scores used to build rfPred meta-score: SIFT, phyloP, MutationTaster, LRT (transformed) and Polyphen2 (corresponding to Polyphen2_HVAR_score). The data frame returned contains these columns:

The following columns are also returned if all.col is TRUE:

Author(s)

Fabienne Jabot-Hanin, Hugo Varet and Jean-Philippe Jais

References

Jabot-Hanin F, Varet H, Tores F and Jais J-P. 2013. rfPred: a new meta-score for functional prediction of missense variants in human exome (submitted).

Examples

# from a data.frame without uniprot protein identifier
data(variant_list_Y)
res=rfPred_scores(variant_list = variant_list_Y[,1:4],
        data = system.file("extdata", "chrY_rfPred.txtz", package="rfPred",mustWork=TRUE),
        index = system.file("extdata", "chrY_rfPred.txtz.tbi", package="rfPred",mustWork=TRUE))
# from a data.frame with uniprot protein identifier
res2=rfPred_scores(variant_list = variant_list_Y,
        data = system.file("extdata", "chrY_rfPred.txtz", package="rfPred",mustWork=TRUE),
        index = system.file("extdata", "chrY_rfPred.txtz.tbi", package="rfPred",mustWork=TRUE))
# from a VCF file
res3=rfPred_scores(variant_list = system.file("extdata", "example.vcf", package="rfPred",mustWork=TRUE),
        data = system.file("extdata", "chrY_rfPred.txtz", package="rfPred",mustWork=TRUE),
        index = system.file("extdata", "chrY_rfPred.txtz.tbi", package="rfPred",mustWork=TRUE))
# from a GRanges object
data(example_GRanges)
res4=rfPred_scores(variant_list = example_GRanges,
        data = system.file("extdata", "chrY_rfPred.txtz", package="rfPred",mustWork=TRUE),
        index = system.file("extdata", "chrY_rfPred.txtz.tbi", package="rfPred",mustWork=TRUE))

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(rfPred)
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: data.table

Attaching package: 'data.table'

The following object is masked from 'package:GenomicRanges':

    shift

The following object is masked from 'package:IRanges':

    shift

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/rfPred/rfPred_scores-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: rfPred_scores
> ### Title: Assign functional prediction rfPred scores to human missense
> ###   variants
> ### Aliases: rfPred_scores rfPred_scores,character-method
> ###   rfPred_scores,data.frame-method rfPred_scores,GRanges-method
> 
> ### ** Examples
> 
> # from a data.frame without uniprot protein identifier
> data(variant_list_Y)
> res=rfPred_scores(variant_list = variant_list_Y[,1:4],
+         data = system.file("extdata", "chrY_rfPred.txtz", package="rfPred",mustWork=TRUE),
+         index = system.file("extdata", "chrY_rfPred.txtz.tbi", package="rfPred",mustWork=TRUE))
> # from a data.frame with uniprot protein identifier
> res2=rfPred_scores(variant_list = variant_list_Y,
+         data = system.file("extdata", "chrY_rfPred.txtz", package="rfPred",mustWork=TRUE),
+         index = system.file("extdata", "chrY_rfPred.txtz.tbi", package="rfPred",mustWork=TRUE))
> # from a VCF file
> res3=rfPred_scores(variant_list = system.file("extdata", "example.vcf", package="rfPred",mustWork=TRUE),
+         data = system.file("extdata", "chrY_rfPred.txtz", package="rfPred",mustWork=TRUE),
+         index = system.file("extdata", "chrY_rfPred.txtz.tbi", package="rfPred",mustWork=TRUE))
> # from a GRanges object
> data(example_GRanges)
> res4=rfPred_scores(variant_list = example_GRanges,
+         data = system.file("extdata", "chrY_rfPred.txtz", package="rfPred",mustWork=TRUE),
+         index = system.file("extdata", "chrY_rfPred.txtz.tbi", package="rfPred",mustWork=TRUE))
Warning message:
In as.data.frame(mcols(x), ...) : Arguments in '...' ignored
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>