tqbrowser: general browsing facility for trans-gQTL

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

Description

Provide a general browsing facility for trans-gQTL.

Usage

tqbrowser(mae, felname, gelname, tiling, tsbra, 
  annovec, band.init = "6q12", ermaset, gwascat, ...)

Arguments

mae	Instance of MultiAssayExperiment-class
felname	character naming the element of mae holding assay features
gelname	character naming the element of mae holding a VcfStack-class instance for genotypes
tiling	a tiling of the genome used to partition large genotype resource
tsbra	an instance of the output of tsByRankAccum that collects association statistics and metadata on general searches for genotype-feature association
annovec	a named character vector mapping between identifiers used to identify features in experiments(mae)[[felname]] and tokens to be used in display – the names of annovec are the rownames to be translated to the associated value in the display.
band.init	an initial tile selection
ermaset	instance of ErmaSet-class
gwascat	instance of gwaswloc-class
...	not currently used

Details

starts a shiny app

Author(s)

VJ Carey <[e-mail]>

Examples

if (interactive()) {
oa = options()$example.ask
options(example.ask=FALSE)
#
# this example assumes you have a working internet connection
# it will collect genotype information from a S3 bucket
# where 1000 genomes VCF resides
#
# obtain infrastructure
#
# message("note: as of Dec 17 2016 this function will trigger transient errors... ignore them") # solved with req()
message("loading packages...")
packs = c("VariantAnnotation", "GenomicFiles", "ggvis", "plotly",
  "Rsamtools", "GenomeInfoDb", "geuvPack", "shiny", "ggplot2",
  "MultiAssayExperiment", "AnnotationHub", "ldblock", "erma")
suppressPackageStartupMessages({
r = sapply(packs, require, character.only=TRUE)
})
stopifnot(all(r))

# use S3 bucket to get genotypes, create VcfStack wrapper
#
message("create VcfStack...")
tf17 = ldblock::s3_1kg("17")
vcst = VcfStack(c("17"=path(tf17)), index=FALSE)
seqlevelsStyle(vcst) = "NCBI"

# obtain expression data for GEUVADIS samples
#
message("obtain expression data...")
if (!exists("geuFPKM")) data(geuFPKM)
data(gen2sym)
seqlevelsStyle(geuFPKM) = "NCBI"
#
# bind to MAE
#
el = ExperimentList(list(geu=geuFPKM, vcf=vcst))
message("create MultiAssayExperiment...")
suppressWarnings({ # samples don't line up between expression and genotype, we know this
mae = MultiAssayExperiment(el, colData=colData(el[[1]]))
})
#
# obtain and clean up cytoband representation
# cyto37n created as follows:
#ah = AnnotationHub()
#cyto37 = ah[["AH5012"]]
#seqlevelsStyle(cyto37) = "NCBI"
#cyto37 = as(cyto37, "GRanges")
#sn = as.character(seqnames(cyto37))
#mcols(cyto37)$name = paste0(sn, mcols(cyto37)$name)
#names(cyto37) = mcols(cyto37)$name
#seqlengths(cyto37)["MT"] = 16569
message("obtain cytoband index...")
data(cyto37n)
data(tbgaOrmdl3)  # saved output of tsByRankAccum, giving association scores
#
message("obtain gwas catalog...")
library(gwascat)
data(ebicat37)
# obtain chromatin state calls from erma
message("obtain chromatin state calls...")
erset = makeErmaSet()
#
# target and invoke browser
#
okba = c("17q12", "17q21.1", "17q21.2")
on.exit(options(example.ask=oa))
print(tqbrowser( mae, "geu", "vcf", cyto37n[okba], 
   tbgaOrmdl3, gen2sym, band.init="17q12", ermaset=erset, gwascat=ebicat37 ))
} # end interactivity check

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