Insure that all scores get tested for association and fix code a bit. (#5)

* Minor debug to run eQTL and pQTL of CAD.

* Removed change intended for local use only and some diff type artefacts that seemed to have been pulled across.

* Replace tab with spaces.

---------

Co-authored-by: aiakvlie <andrii.iakovliev@ed.ac.uk>

Author: dlipschu

association.R

@@ -44,6 +44,11 @@ if(newrun) {
     load(file.path(output.dir, "coeffs.RData"))
 }
 
+# Make sure that regressions were run for all scores
+if(nrow(coeffs) != length(scoreids)){
+    stop('Number of associations does not equal the number of scores.')
+}
+
 ## merge coeffs with scores metadata
 if (analysis=="eQTL")
     scoresinfo <- allscores.info
@@ -111,4 +116,4 @@ coeffs.wide <- genes.info[, .(gene_symbol, gene_biotype, is.t1dgene, is.t2dgene,
 ## annotate genes by whether they are known cause for monogenic diabetes
 coeffs.wide[, monogenic := ifelse(gene_symbol %in% t1d.monogenes, "+", ".")]
 
-save(coeffs.wide, file=file.path(output.dir, "coeffs.wide.RData")
+save(coeffs.wide, file=file.path(output.dir, "coeffs.wide.RData"))

gw.trans.scores.R

@@ -55,7 +55,7 @@ if (include.hla) {
 #' sum up all scores to generate a single genome-wide score also including cis
 #' effects.
 ##------------------------------------------------------------------------------
-if (analysis == "immunecells")) {
+if (analysis == "immunecells") {
     cat("Immune cells cannot be currently annotated. Skipping.\n")
     ans[, trait_name := gsub(":", "_", trait_name)]
     ans[, trait_name := gsub(" ", "_", trait_name)]

qtl.metadata.R

@@ -99,7 +99,6 @@ if (analysis == "eQTL") {
     ## recode cis-x as cis but keep an indicator for cis-x
     allscores.info[, cisx := qtl_type=="cis-x"]
     allscores.info[qtl_type=="cis-x", qtl_type := "cis"]
-    setnames(allscores.info, "gene_chrom", "chromosome")
 
     table(allscores.info$matrix.colname %in% colnames(genome.wide.scores))
     ## remove rows not matched in scores table