bindmaf {GGtools} | R Documentation

## bind testing metadata to a best.cis.eQTLs result

### Description

bind testing metadata to a best.cis.eQTLs result

### Usage

    meta.bindmaf (smpackvec=c("GGdata", "hmyriB36"),
         smchr="20", obj, usemaxMAF=FALSE, SSgen=GGBase::getSS)

### Arguments

`smpackvec` | a vector of candidate package names (potential smpack arguments to `getSS` for metaanalysis across populations or tissues
`smchr` | the chromosome name as used in the names of the `smList` output for the `getSS` result
`obj` | an instance of `mcwBestCis-class` generated using the package named in `smpack`
`usemaxMAF` | if TRUE, label a SNP with maximum MAF observed across populations, otherwise compute the MAF for the combined genotypes across populations represented by the various smlSet instances generated with the `smpackvec` spec.
`SSgen` | function to be used to create smlSet instance for testing – in general, GGBase::getSS has been used to pull the ExpressionSet and SnpMatrix data from a named package, but in some cases a specialize task is needed to create the desired smlSet. Whatever is passed to SSgen must return an smlSet instance.

### Details

computes the MAF of most highly associated SNP per gene, and distance between that SNP and the transcription limits of the gene, assigning 0 for this if the SNP lies within the transcription limits

### Value

a GRanges instance

### Note

This will be used to stratify the permuted scores.

### Examples

    ## Not run:
     b1 = best.cis.eQTLs(chr="20")  # sharply filtered
     b1b = bindmaf(obj=b1)

    ## End(Not run)

[Package GGtools version 5.16.0 Index]