From 0bfe2990ce31fbd808b680a883619575d864aef5 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 25 May 2021 20:28:02 +0000
Subject: Add rqtl_wrapper.R script and necessary imports to guix.scm

---
 scripts/rqtl_wrapper.R | 204 +++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 204 insertions(+)
 create mode 100644 scripts/rqtl_wrapper.R

(limited to 'scripts')

diff --git a/scripts/rqtl_wrapper.R b/scripts/rqtl_wrapper.R
new file mode 100644
index 0000000..ae970d4
--- /dev/null
+++ b/scripts/rqtl_wrapper.R
@@ -0,0 +1,204 @@
+library(optparse)
+library(qtl)
+library(stringi)
+library(stringr)
+
+tmp_dir = Sys.getenv("TMPDIR")
+
+option_list = list(
+  make_option(c("-g", "--geno"), type="character", help=".geno file containing a dataset's genotypes"),
+  make_option(c("-p", "--pheno"), type="character", help="File containing two columns - sample names and values"),
+  make_option(c("-c", "--addcovar"), action="store_true", default=NULL, help="Use covariates (included as extra columns in the phenotype input file)"),
+  make_option(c("--model"), type="character", default="normal", help="Mapping Model - Normal or Non-Parametric"),
+  make_option(c("--method"), type="character", default="hk", help="Mapping Method - hk (Haley Knott), ehk (Extended Haley Knott), mr (Marker Regression), em (Expectation-Maximization), imp (Imputation)"),
+  make_option(c("-i", "--interval"), action="store_true", default=NULL, help="Use interval mapping"),
+  make_option(c("--nperm"), type="integer", default=0, help="Number of permutations"),
+  make_option(c("-s", "--scale"), type="character", default="mb", help="Mapping scale - Megabases (Mb) or Centimorgans (cM)"),
+  make_option(c("--control"), type="character", default=NULL, help="Name of marker (contained in genotype file) to be used as a control"),
+  make_option(c("-o", "--outdir"), type="character", default=file.path(tmp_dir, "output"), help="Directory in which to write result file"),
+  make_option(c("-f", "--filename"), type="character", default=NULL, help="Name to use for result file"),
+  make_option(c("-v", "--verbose"), action="store_true", default=NULL, help="Show extra information")
+);
+
+opt_parser = OptionParser(option_list=option_list);
+opt = parse_args(opt_parser);
+
+verbose_print <- function(...){
+  if (!is.null(opt$verbose)) {
+    for(item in list(...)){
+      cat(item)
+    }
+    cat("\n")
+  }
+}
+
+if (is.null(opt$geno) || is.null(opt$pheno)){
+  print_help(opt_parser)
+  stop("Both a genotype and phenotype file must be provided.", call.=FALSE)
+}
+
+geno_file = opt$geno
+pheno_file = opt$pheno
+
+# Generate randomized filename for cross object
+cross_file = file.path(tmp_dir, "cross", paste(stri_rand_strings(1, 8), ".cross", sep = ""))
+
+trim <- function( x ) { gsub("(^[[:space:]]+|[[:space:]]+$)", "", x) }
+
+get_geno_code <- function(header, name = 'unk'){
+  mat = which(unlist(lapply(header,function(x){ length(grep(paste('@',name,sep=''), x)) })) == 1)
+  return(trim(strsplit(header[mat],':')[[1]][2]))
+}
+
+geno_to_csvr <- function(genotypes, trait_names, trait_vals, out, sex = NULL,
+                         mapping_scale = "Mb", verbose = FALSE){
+  # Assume a geno header is not longer than 40 lines
+  header = readLines(genotypes, 40)
+
+  # Major hack to skip the geno headers
+  toskip = which(unlist(lapply(header, function(x){ length(grep("Chr\t", x)) })) == 1) - 1
+
+  type <- get_geno_code(header, 'type')
+
+  # Get the genotype codes
+  if(type == '4-way'){
+    genocodes <- NULL
+  } else {
+    genocodes <- c(get_geno_code(header, 'mat'), get_geno_code(header, 'het'),
+                   get_geno_code(header, 'pat'))
+  }
+  genodata <- read.csv(genotypes, sep='\t', skip=toskip, header=TRUE,
+                       na.strings=get_geno_code(header,'unk'),
+                       colClasses='character', comment.char = '#')
+
+  verbose_print('Genodata:', toskip, " ", dim(genodata), genocodes, '\n')
+
+  # If there isn't a sex phenotype, treat all as males
+  if(is.null(sex)) sex <- rep('m', (ncol(genodata)-4))
+
+  cross_items = list()
+
+  # Add trait and covar phenotypes
+  for (i in 1:length(trait_names)){
+    cross_items[[i]] <- c(trait_names[i], '', '', unlist(trait_vals[[i]]))
+  }
+
+  # Sex phenotype for the mice
+  cross_items[[length(trait_names) + 1]] <- c('sex', '', '', sex)
+  # Genotypes
+  cross_items[[length(trait_names) + 2]] <- cbind(genodata[,c('Locus','Chr', mapping_scale)],
+                                                  genodata[, 5:ncol(genodata)])
+
+  out_csvr <- do.call(rbind, cross_items)
+
+  # Save it to a file
+  write.table(out_csvr, file=out, row.names=FALSE, col.names=FALSE, quote=FALSE, sep=',')
+
+  # Load the created cross file using R/qtl read.cross
+  if (type == '4-way') {
+    verbose_print('Loading in as 4-WAY\n')
+    cross = read.cross(file=out, 'csvr', genotypes=NULL, crosstype="4way")
+  } else if(type == 'f2') {
+    verbose_print('Loading in as F2\n')
+    cross = read.cross(file=out, 'csvr', genotypes=genocodes, crosstype="f2")
+  } else {
+    verbose_print('Loading in as normal\n')
+    cross = read.cross(file=out, 'csvr', genotypes=genocodes)
+  }
+  if (type == 'riset') {
+    # If its a RIL, convert to a RIL in R/qtl
+    verbose_print('Converting to RISELF\n')
+    cross <- convert2riself(cross)
+  }
+
+  return(cross)
+}
+
+create_marker_covars <- function(the_cross, control_marker){
+  #' Given a string of one or more marker names (comma separated), fetch
+  #' the markers' values from the genotypes and return them as vectors/a vector
+  #' of values
+
+  # In case spaces are added in the string of marker names
+  covariate_names <- strsplit(str_replace(control_marker, " ", ""), ",")
+
+  genotypes <- pull.geno(the_cross)
+  covariates_in_geno <- which(covariate_names %in% colnames(genotypes))
+  covariate_names <- covariate_names[covariates_in_geno]
+  marker_covars <- genotypes[, unlist(covariate_names)]
+
+  return(marker_covars)
+}
+
+# Get phenotype vector from input file
+df <- read.table(pheno_file, na.strings = "x", header=TRUE, check.names=FALSE)
+sample_names <- df$Sample
+trait_names <- colnames(df)[2:length(colnames(df))]
+
+trait_vals <- vector(mode = "list", length = length(trait_names))
+for (i in 1:length(trait_names)) {
+  this_trait <- trait_names[i]
+  this_vals <- df[this_trait]
+  trait_vals[[i]] <- this_vals
+}
+
+# Since there will always only be one non-covar phenotype, its name will be in the first column
+pheno_name = unlist(trait_names)[1]
+
+verbose_print('Generating cross object\n')
+cross_object = geno_to_csvr(geno_file, trait_names, trait_vals, cross_file)
+
+# Calculate genotype probabilities
+if (!is.null(opt$interval)) {
+  verbose_print('Calculating genotype probabilities with interval mapping\n')
+  cross_object <- calc.genoprob(cross_object, step=5, stepwidth="max")
+} else {
+  verbose_print('Calculating genotype probabilities\n')
+  cross_object <- calc.genoprob(cross_object)
+}
+
+# Pull covariates out of cross object, if they exist
+covars = vector()
+if (!is.null(opt$addcovar)) {
+  covar_names = trait_names[2:length(trait_names)]
+  covars <- pull.pheno(cross_object, covar_names)
+}
+
+# If a marker name is supplied as covariate, get its vector of values and add them as a covariate
+if (!is.null(opt$control)) {
+  marker_covars = create_marker_covars(cross_object, opt$control)
+  covars <- cbind(covars, marker_covars)
+}
+
+# Calculate permutations
+if (opt$nperm > 0) {
+  if (!is.null(opt$filename)){
+    perm_out_file = file.path(opt$outdir, paste("PERM_", opt$filename, sep = ""))
+  } else {
+    perm_out_file = file.path(opt$outdir, paste(pheno_name, "_PERM_", stri_rand_strings(1, 8), ".csv", sep = ""))
+  }
+
+  if (!is.null(opt$addcovar) || !is.null(opt$control)){
+    verbose_print('Running permutations with cofactors\n')
+    perm_results = scanone(cross_object, pheno.col=1, addcovar=covars, n.perm=opt$nperm, model=opt$model, method=opt$method)
+  } else {
+    verbose_print('Running permutations\n')
+    perm_results = scanone(cross_object, pheno.col=1, n.perm=opt$nperm, model=opt$model, method=opt$method)
+  }
+  write.csv(perm_results, perm_out_file)
+}
+
+if (!is.null(opt$filename)){
+  out_file = file.path(opt$outdir, opt$filename)
+} else {
+  out_file = file.path(opt$outdir, paste(pheno_name, "_", stri_rand_strings(1, 8), ".csv", sep = ""))
+}
+
+if (!is.null(opt$addcovar) || !is.null(opt$control)){
+  verbose_print('Running scanone with cofactors\n')
+  qtl_results = scanone(cross_object, pheno.col=1, addcovar=covars, model=opt$model, method=opt$method)
+} else {
+  verbose_print('Running scanone\n')
+  qtl_results = scanone(cross_object, pheno.col=1, model=opt$model, method=opt$method)
+}
+write.csv(qtl_results, out_file)
\ No newline at end of file
-- 
cgit v1.2.3


From 9b8fb0f63114119e58663a3e7fee352ce7375fb4 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 26 May 2021 15:09:00 +0000
Subject: Added option for enabling permutation strata

Fixed issue where covariates with numerical names were being ignored

Fixed issue where the hash filename wasn't being used for the permutation output
---
 scripts/rqtl_wrapper.R | 51 +++++++++++++++++++++++++++++++++++++-------------
 1 file changed, 38 insertions(+), 13 deletions(-)

(limited to 'scripts')

diff --git a/scripts/rqtl_wrapper.R b/scripts/rqtl_wrapper.R
index ae970d4..f7e0406 100644
--- a/scripts/rqtl_wrapper.R
+++ b/scripts/rqtl_wrapper.R
@@ -13,6 +13,7 @@ option_list = list(
   make_option(c("--method"), type="character", default="hk", help="Mapping Method - hk (Haley Knott), ehk (Extended Haley Knott), mr (Marker Regression), em (Expectation-Maximization), imp (Imputation)"),
   make_option(c("-i", "--interval"), action="store_true", default=NULL, help="Use interval mapping"),
   make_option(c("--nperm"), type="integer", default=0, help="Number of permutations"),
+  make_option(c("--pstrata"), action="store_true", default=NULL, help="Use permutation strata (stored as final column/vector in phenotype input file)"),
   make_option(c("-s", "--scale"), type="character", default="mb", help="Mapping scale - Megabases (Mb) or Centimorgans (cM)"),
   make_option(c("--control"), type="character", default=NULL, help="Name of marker (contained in genotype file) to be used as a control"),
   make_option(c("-o", "--outdir"), type="character", default=file.path(tmp_dir, "output"), help="Directory in which to write result file"),
@@ -135,15 +136,17 @@ df <- read.table(pheno_file, na.strings = "x", header=TRUE, check.names=FALSE)
 sample_names <- df$Sample
 trait_names <- colnames(df)[2:length(colnames(df))]
 
+# Since there will always only be one non-covar phenotype, its name will be in the first column
+pheno_name = unlist(trait_names)[1]
+
 trait_vals <- vector(mode = "list", length = length(trait_names))
 for (i in 1:length(trait_names)) {
   this_trait <- trait_names[i]
   this_vals <- df[this_trait]
   trait_vals[[i]] <- this_vals
-}
 
-# Since there will always only be one non-covar phenotype, its name will be in the first column
-pheno_name = unlist(trait_names)[1]
+  trait_names[i] = paste("T_", this_trait, sep = "")
+}
 
 verbose_print('Generating cross object\n')
 cross_object = geno_to_csvr(geno_file, trait_names, trait_vals, cross_file)
@@ -158,12 +161,24 @@ if (!is.null(opt$interval)) {
 }
 
 # Pull covariates out of cross object, if they exist
-covars = vector()
+covars = vector(mode = "list", length = length(trait_names) - 1)
 if (!is.null(opt$addcovar)) {
-  covar_names = trait_names[2:length(trait_names)]
+  #If perm strata are being used, it'll be included as the final column in the phenotype file
+  if (!is.null(opt$pstrata)) {
+    covar_names = trait_names[3:length(trait_names) - 1]
+  } else {
+    covar_names = trait_names[3:length(trait_names)]
+  }
   covars <- pull.pheno(cross_object, covar_names)
 }
 
+# Pull permutation strata out of cross object, if it is being used
+perm_strata = vector()
+if (!is.null(opt$pstrata)) {
+  strata_col = trait_names[length(trait_names)]
+  perm_strata <- pull.pheno(cross_object, strata_col)
+}
+
 # If a marker name is supplied as covariate, get its vector of values and add them as a covariate
 if (!is.null(opt$control)) {
   marker_covars = create_marker_covars(cross_object, opt$control)
@@ -173,17 +188,27 @@ if (!is.null(opt$control)) {
 # Calculate permutations
 if (opt$nperm > 0) {
   if (!is.null(opt$filename)){
-    perm_out_file = file.path(opt$outdir, paste("PERM_", opt$filename, sep = ""))
+    perm_out_file = file.path(opt$outdir, paste("PERM_", opt$filename, sep = "" ))
   } else {
-    perm_out_file = file.path(opt$outdir, paste(pheno_name, "_PERM_", stri_rand_strings(1, 8), ".csv", sep = ""))
+    perm_out_file = file.path(opt$outdir, paste(pheno_name, "_PERM_", stri_rand_strings(1, 8), sep = ""))
   }
 
   if (!is.null(opt$addcovar) || !is.null(opt$control)){
-    verbose_print('Running permutations with cofactors\n')
-    perm_results = scanone(cross_object, pheno.col=1, addcovar=covars, n.perm=opt$nperm, model=opt$model, method=opt$method)
+    if (!is.null(opt$pstrata)) {
+      verbose_print('Running permutations with cofactors and strata\n')
+      perm_results = scanone(cross_object, pheno.col=1, addcovar=covars, n.perm=opt$nperm, perm.strata=perm_strata, model=opt$model, method=opt$method)
+    } else {
+      verbose_print('Running permutations with cofactors\n')
+      perm_results = scanone(cross_object, pheno.col=1, addcovar=covars, n.perm=opt$nperm, model=opt$model, method=opt$method)
+    }
   } else {
-    verbose_print('Running permutations\n')
-    perm_results = scanone(cross_object, pheno.col=1, n.perm=opt$nperm, model=opt$model, method=opt$method)
+    if (!is.null(opt$pstrata)) {
+      verbose_print('Running permutations with strata\n')
+      perm_results = scanone(cross_object, pheno.col=1, n.perm=opt$nperm, perm.strata=perm_strata, model=opt$model, method=opt$method)
+    } else {
+      verbose_print('Running permutations\n')
+      perm_results = scanone(cross_object, pheno.col=1, n.perm=opt$nperm, model=opt$model, method=opt$method)
+    }
   }
   write.csv(perm_results, perm_out_file)
 }
@@ -191,7 +216,7 @@ if (opt$nperm > 0) {
 if (!is.null(opt$filename)){
   out_file = file.path(opt$outdir, opt$filename)
 } else {
-  out_file = file.path(opt$outdir, paste(pheno_name, "_", stri_rand_strings(1, 8), ".csv", sep = ""))
+  out_file = file.path(opt$outdir, paste(pheno_name, "_", stri_rand_strings(1, 8), sep = ""))
 }
 
 if (!is.null(opt$addcovar) || !is.null(opt$control)){
@@ -201,4 +226,4 @@ if (!is.null(opt$addcovar) || !is.null(opt$control)){
   verbose_print('Running scanone\n')
   qtl_results = scanone(cross_object, pheno.col=1, model=opt$model, method=opt$method)
 }
-write.csv(qtl_results, out_file)
\ No newline at end of file
+write.csv(qtl_results, out_file)
-- 
cgit v1.2.3