traitsManh {gwascat} | R Documentation |
use ggbio facilities to display GWAS results for selected traits in genomic coordinates
traitsManh(gwr, selr = GRanges(seqnames = "chr17", IRanges(3e+07, 5e+07)), traits = c("Asthma", "Parkinson's disease", "Height", "Crohn's disease"), truncmlp = 25, ...)
gwr |
GRanges instance as managed by the gwaswloc container design, with Disease.Trait and Pvalue\_mlog among elementMetadata columns |
selr |
A GRanges instance to restrict the |
traits |
Character vector of traits to be exhibited; GWAS results with traits not among these will be labeled “other”. |
truncmlp |
Maximum value of -log10 p to be displayed; in the raw data this ranges to the hundreds and can cause bad compression. |
... |
not currently used |
uses a ggbio autoplot
autoplot value
An xlab is added, concatenating genome tag with seqnames tag.
VJ Carey <stvjc@channing.harvard.edu>
# do a p-value truncation if you want to reduce compression data(ebicat38) library(GenomeInfoDb) seqlevelsStyle(ebicat38) = "UCSC" traitsManh(ebicat38)