transBrowse: shiny app to exhibit genotype:genomic feature distributions

In gQTLstats: gQTLstats: computationally efficient analysis for eQTL and allied studies

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

gQTLstats documentation built on Nov. 8, 2020, 7:53 p.m.