Associate genotypes with user regions from a SNPhood object.

Description

The function associateGenotypes associates genotypes with SNP regions as defined in a SNPhood object. It is possible to assign genotypes only for a subset of datasets as defined in a SNPhood object. To avoid any ambiguities, a 1:1 for genotype and dataset mapping must be given (ses below).

Usage

associateGenotypes(SNPhood.o, genotypeMapping, verbose = TRUE)

Arguments

Value

Object of class SNPhood with the genotype information added to the slot annotation, element genotype. You may retrieve it via the accessor function annotation.

Examples

data(SNPhood.o, package="SNPhood")
fileGenotypes = list.files(pattern = "*genotypes*",system.file("extdata", package = "SNPhoodData"), full.names = TRUE)
mapping = data.frame(samples = annotationDatasets(SNPhood.o), genotypeFile = rep(fileGenotypes, 2), sampleName = c("NA10847", "NA12890"))
SNPhood.o = associateGenotypes(SNPhood.o, mapping)

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)

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> library(SNPhood)
Loading required package: GenomicRanges
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
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Rsamtools
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

Loading required package: checkmate

------------------------------------------------------------------------------------------------------------------
|       Welcome to the SNPhood package and thank you for using our software. This is SNPhood version 1.2.2.      |
| See the vignettes (type browseVignettes("SNPhood") or the help pages for how to use SNPhood for your analyses. |
|       Thank you for using our software. Please do not hesitate to contact us if there are any questions.       |
------------------------------------------------------------------------------------------------------------------

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/SNPhood/associateGenotypes.Rd_%03d_medium.png", width=480, height=480)
> ### Name: associateGenotypes
> ### Title: Associate genotypes with user regions from a _SNPhood_ object.
> ### Aliases: associateGenotypes
> 
> ### ** Examples
> 
> data(SNPhood.o, package="SNPhood")
> fileGenotypes = list.files(pattern = "*genotypes*",system.file("extdata", package = "SNPhoodData"), full.names = TRUE)
> mapping = data.frame(samples = annotationDatasets(SNPhood.o), genotypeFile = rep(fileGenotypes, 2), sampleName = c("NA10847", "NA12890"))
> SNPhood.o = associateGenotypes(SNPhood.o, mapping)
Check object integrity and validity. For large objects, this may take some time. Use the function changeObjectIntegrityChecking to disable this check for the object.

 Import genotypes from file /home/ddbj/local/lib64/R/library/SNPhoodData/extdata/genotypes.vcf.gz. This may take a while...

 Common samples found in file /home/ddbj/local/lib64/R/library/SNPhoodData/extdata/genotypes.vcf.gz. Extract genotypes for samples NA10847,NA12890.
 Found and imported 172 SNPs with genotype information across all samples out of all 174 SNPs as defined in the SNPhood object.
The individual genotypes have been added to the annotation.
 Check for genotype mismatches for file GM10847
Found 0 mismatches between the genotypes from the BAM file reads and the VCF information for sample GM10847
 Check for genotype mismatches for file GM12890
Found 0 mismatches between the genotypes from the BAM file reads and the VCF information for sample GM12890
Found 0 mismatches between the genotypes from the BAM file reads and the VCF information across all files
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>