transBrowse {gQTLstats} | R Documentation

## shiny app to exhibit genotype:genomic feature distributions

### Description

exhibit genotype:genomic feature distributions with a shiny app

### Usage

    transBrowse(tbg, anno, tivcf, se, title = "trans eQTL")
    transBrowse2(tbga, annovec, tivcf, se, title = "trans eQTL", maxrank=3)

### Arguments

`tbg` | filtered output of `tsByRankAccum`, see example
`tbga` | filtered output of `tsByRankAccum`, see example
`anno` | a vector with 'feature symbols' (e.g.,, gene symbols) as values and 'feature names' (elements of rownames of `se`, e.g., ENSEMBLE gene ids) as names
`annovec` | a vector with 'feature symbols' (e.g.,, gene symbols) as values and 'feature names' (elements of rownames of `se`, e.g., ENSEMBLE gene ids) as names
`tivcf` | reference to Tabix-indexed VCF
`se` | SummarizedExperiment instance with rowname coincident with `anno` and `tbg[["allfeats"]]`
`title` | optional string for title panel
`maxrank` | transBrowse2 works with the tsByRankAccum function that collects scores down to a specified rank. This parameter specifies the boundary.

### Details

This function is under development. The intention is to allow convenient visualization of off-chromosome genotype-feature relationships. AllAssoc collects association scores SNP-wise, and saves the largest "K" scores obtained, along with feature identity and location metadata. The largest score obtained for a given SNP is the rank 1 association, the next largest is rank 2, and so on.

### Examples

    ## Not run:
     # consider the following filtering utility
     tbfilt = function(tbg, seqnames.="17", minMAF=.1, minabsodist = 1e7,
        nrec=1000) {
       tbg = tbg[ which(as.character(seqnames(tbg)) %in% seqnames.) ]
       tbg = tbg[ which(tbg$MAF > minMAF & abs(tbg$obsdist) > minabsodist) ]
       tbg[ order(tbg$scores, decreasing=TRUE) ][1:nrec]
     }
     #
       registerDoSEQ()
       library(geuvStore2)
       r17 = g17transRegistry()
       g17 = TransStore(list(r17))
       tbg = tbfilt(tsByRankAccum(g17, 3, mcol2keep=c("REF", "snp", "MAF"))) # 1000 records
       tf17 = ldblock::s3_1kg("17")  # uses S3 bucket
       require(geuvPack)
       require(shiny)
       if (!exists("geuFPKM")) data(geuFPKM)
       if (!exists("gencodeV12")) data(gencodeV12)
       data(gen2sym)
       transBrowse2( tbg, gen2sym, tf17, geuFPKM, title="trans GEUV chr17")

    ## End(Not run) # end dontrun

[Package gQTLstats version 1.12.0 Index]