Open dalloliogm opened 6 years ago
regionplot should give a better error output when the plot fails because there are not enough SNPs in the region.
This may happen for several reasons - in my case, because the coordinates where from a wrong reference genome.
> regionplot("eqtl_gene_blood_zhernakova", chrom = '6', pos = 32566577, surround = 5e3, ensemblid = 'ENSG00000013573') analysis [ eqtl_gene_blood_zhernakova ] requires entity type [ ensg ] Inferred entity [ ENSG00000013573 ] from Ensembl gene id [ ENSG00000013573 ] analysis [ eqtl_gene_blood_zhernakova ] requires entity type [ ensg ] Recognized entity [ ENSG00000013573 ] as Ensembl gene id No signals from conditional/joint analyses overlap this region Warning message in min(which(ps >= cred * ps[length(ps)])): “no non-missing arguments to min; returning Inf” Error in rgb((255 - 171) * posterior/max(posterior) + 171, (0 - 171) * : color intensity NA, not in 0:255 Traceback: 1. regionplot("eqtl_gene_blood_zhernakova", chrom = "6", pos = 32566577, . surround = 5000, ensemblid = "ENSG00000013573") 2. within(pvals, { . posterior <- norm1(abf.Wakefield(beta, se, priorsd = 1, log = TRUE), . log = TRUE) . posterior <- ifelse(!is.na(posterior), posterior, 0) . c95 <- credset(posterior) . colour <- rgb((255 - 171) * posterior/max(posterior) + 171, . (0 - 171) * posterior/max(posterior) + 171, (0 - 171) * . posterior/max(posterior) + 171, alpha = 127, maxColorValue = 255) . }) 3. within.data.frame(pvals, { . posterior <- norm1(abf.Wakefield(beta, se, priorsd = 1, log = TRUE), . log = TRUE) . posterior <- ifelse(!is.na(posterior), posterior, 0) . c95 <- credset(posterior) . colour <- rgb((255 - 171) * posterior/max(posterior) + 171, . (0 - 171) * posterior/max(posterior) + 171, (0 - 171) * . posterior/max(posterior) + 171, alpha = 127, maxColorValue = 255) . }) 4. eval(substitute(expr), e) 5. eval(substitute(expr), e) 6. rgb((255 - 171) * posterior/max(posterior) + 171, (0 - 171) * . posterior/max(posterior) + 171, (0 - 171) * posterior/max(posterior) + . 171, alpha = 127, maxColorValue = 255)
regionplot should give a better error output when the plot fails because there are not enough SNPs in the region.
This may happen for several reasons - in my case, because the coordinates where from a wrong reference genome.