cisRun-like entity to which additional annotation
will be bound by addgwhit or add878
gwtagger
GRanges like gwastagger in gwascat data elements
traitFilter
function that returns a gwastagger-like GRanges, see
inflammFilter
vname
name to be used for new data.table column added by
addgwhit
Details
cisScores (All.cis)
returns score statistics for assocations of all SNP cis to genes,
in a GRanges instance, with range names given by probes; metadata supplied
SNP location, name, and score
cisAssoc targets SummarizedExperiment instances for molecular
phenotype measures and VCF for variant data
addgwhit and add878 will use
GWAS hit information or ChromHMM labeling to annotation
ranges
Value
for cisScores: instance of cisRun-class
for cisAssoc: a GRanges with information on observed and
permuted test scores per locus/feature pair
Author(s)
VJ Carey <stvjc@channing.harvard.edu>
Examples
## Not run:
cc = new("CisConfig")
chrnames(cc) = "21"
genome(cc) = "hg19"
lkp = try(library(parallel))
if (!inherits(lkp, "try-error")) {
nc = min(10, detectCores())
options(mc.cores=nc)
geneApply(cc) = mclapply
}
estimates(cc) = FALSE
set.seed(1234)
unix.time(f1 <- cisScores( cc ))
#
# demonstrate adding annotation on chromatin state and gwas status
#
eprops = function(ans) {
#
# only adds fields to values() of the input
#
data(hmm878)
ac = as.character
eqr = GRanges(ac(seqnames(ans)), IRanges(ans$snplocs, width=1))
fo = findOverlaps(eqr, hmm878)
chromcat878 = factor(rep("none", length(ans)), levels=c(unique(hmm878$name), "none"))
chromcat878[ queryHits(fo) ] = factor(hmm878$name[subjectHits(fo)])
ans$chromcat878 = chromcat878
if (require(gwascat)) {
data(gwastagger)
isgwashit = 1*(overlapsAny(eqr, gwastagger) | ans$snp
ans$isgwashit = isgwashit
}
ans
}
extraProps(cc) = eprops
set.seed(1234)
unix.time(f2 <- cisScores( cc ))
#
#
inflammFilter # to make more restrictive predicate for prediction
## End(Not run)