All.cis {GGtools} | R Documentation |
function that computes score tests for all SNP cis to genes, with flexible filtering
cisScores( config = new("CisConfig"), ... ) All.cis( config = new("CisConfig"), ... ) addgwhit(ans, traitFilter=force, vname="isgwashit") add878(ans) inflammFilter(gwtagger)
config |
instance of class |
... |
passed to eqtlTests |
ans |
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
|
vname |
name to be used for new data.table column added by addgwhit |
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
for cisScores: instance of cisRun-class
for cisAssoc: a GRanges with information on observed and permuted test scores per locus/feature pair
VJ Carey <stvjc@channing.harvard.edu>
## 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) system.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) system.time(f2 <- cisScores( cc )) # # inflammFilter # to make more restrictive predicate for prediction ## End(Not run)