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author | dereeper |
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date | Mon, 16 Apr 2018 08:50:05 -0400 |
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#!/usr/bin/perl use strict; use Getopt::Long; use Bio::SeqIO; my $usage = qq~Usage:$0 <args> [<opts>] where <args> are: -g, --geno <Genotype input> -i, --info <SNP information. Genome position.> -p, --pheno <Phenotype input> -o, --out <output name> -d, --directory <directory for MLMM R libraries> -s, --step_number <number of steps. Maximum: 20. Default: 10> -m, --method <Method: mbonf or extBIC. Default: mbonf> ~; $usage .= "\n"; my ($geno,$map,$pheno,$out,$dir,$steps,$method); GetOptions( "geno=s" => \$geno, "info=s" => \$map, "pheno=s" => \$pheno, "out=s" => \$out, "dir=s" => \$dir, "steps=s" => \$steps, "method=s" => \$method ); die $usage if ( !$geno || !$map || !$pheno || !$out || !$dir || !$steps || !$method); my $max_steps = 10; my $plot_opt = "mbonf"; if ($method && $method ne 'mbonf' && $method ne 'extBIC') { print "Aborted: Method must be mbonf or extBIC.\n"; exit; } else { $plot_opt = $method; } if ($steps && $steps !~/\d+/ && $steps > 20 && $steps < 2) { print "Aborted: Number of steps must be greater than 2 and lower than 20.\n"; exit; } else { $max_steps = $steps; } my $chunk = 2; my $RSCRIPT_EXE = "Rscript"; my $R_DIR = $dir; my $head_trait = `head -1 $pheno`; my @headers_traits = split(/\t/,$head_trait); my $trait_name = $headers_traits[1]; open( my $RCMD, ">rscript" ) or throw Error::Simple($!); print $RCMD "Y_file <- \"" . $pheno . "\"\n"; print $RCMD "X_file <- \"" . $geno . "\"\n"; if($map) { print $RCMD "map_file <- \"$map\"\n"; print $RCMD "map <- read.table(map_file, sep = \"\\t\", header = T)\n"; } print $RCMD "mlmm_data = list()\n"; print $RCMD "mlmm_data\$chunk <- $chunk\n"; print $RCMD "mlmm_data\$maxsteps <- $max_steps\n"; print $RCMD "genot <- read.table(X_file, sep = \"\\t\", header = T)\n"; print $RCMD "genot_mat <- as.matrix(genot[, 2:ncol(genot)])\n"; print $RCMD "rownames(genot_mat) <- genot\$Ind_id\n"; print $RCMD "phenot <- read.table(Y_file, sep = \"\\t\", header = T)\n"; # missing data imputation print $RCMD "genot_imp <- genot_mat\n"; print $RCMD "average <- colMeans(genot_imp, na.rm = T)\n"; print $RCMD "for (i in 1:ncol(genot_imp)){genot_imp[is.na(genot_imp[,i]), i] <- average[i]}\n"; # kinship matrix computation print $RCMD "average <- colMeans(genot_imp, na.rm = T)\n"; print $RCMD "stdev <- apply(genot_imp, 2, sd)\n"; print $RCMD "genot_stand <- sweep(sweep(genot_imp, 2, average, \"-\"), 2, stdev, \"/\")\n"; print $RCMD "K_mat <- (genot_stand %*% t(genot_stand)) / ncol(genot_stand)\n"; print $RCMD "write.table(K_mat, '$out.kinship', sep='\\t', dec='.', quote=F, col.names=T, row.names=T)\n"; print $RCMD "source(\"" . $R_DIR. "/mlmm.r\")\n"; print $RCMD "source(\"" . $R_DIR. "/emma.r\")\n"; # mlmm print $RCMD "mygwas <- mlmm(Y = phenot\$$trait_name, X = genot_imp, K = K_mat, nbchunks=mlmm_data\$chunk, maxsteps=mlmm_data\$maxsteps)\n"; # plots print $RCMD "pdf('$out.pdf')\n"; print $RCMD "plot_step_table(mygwas, \"h2\")\n"; print $RCMD "plot_step_table(mygwas, \"extBIC\")\n"; print $RCMD "plot_step_table(mygwas, \"maxpval\")\n"; print $RCMD "plot_step_RSS(mygwas)\n"; # for (my $j = 1; $j <= ($max_steps - 1); $j++) # { # print $RCMD "plot_fwd_GWAS(mygwas, step = $j, snp_info = map, pval_filt = 0.1)\n"; # } print $RCMD "plot_opt_GWAS(mygwas, opt = \"extBIC\", snp_info = map, pval_filt = 0.1)\n"; print $RCMD "plot_opt_GWAS(mygwas, opt = \"mbonf\", snp_info = map, pval_filt = 0.1)\n"; #print $RCMD "qqplot_fwd_GWAS(mygwas, nsteps = mlmm_data\$maxsteps)\n"; print $RCMD "qqplot_opt_GWAS(mygwas, opt = \"extBIC\")\n"; print $RCMD "qqplot_opt_GWAS(mygwas, opt = \"mbonf\")\n"; # outputs print $RCMD "write.table(mygwas\$RSSout, '$out.rss', sep='\\t', dec='.', quote=F, col.names=T, row.names=F)\n"; print $RCMD "write.table(mygwas\$step_table, '$out.steptable', sep='\\t', dec='.', quote=F, col.names=T, row.names=F)\n"; $plot_opt = "\$opt_" . $plot_opt; print $RCMD "pval = mygwas" . $plot_opt . "\$out\n"; print $RCMD "colnames(pval) = c(\"Marker_name\", \"Pvalue\")\n"; print $RCMD "info_tmp = map\n"; print $RCMD "colnames(info_tmp) = c(\"Marker_name\", \"Chr\", \"Pos\")\n"; print $RCMD "res_asso = pval\n"; print $RCMD qq~ if(exists("info_tmp")){ res_asso = merge(info_tmp, res_asso, by="Marker_name") if( !is.element("Trait", colnames(info_tmp)) ){ m = matrix(data="traitname", ncol=1, nrow=nrow(res_asso), dimnames=list(c(), c("Trait"))) res_asso = cbind(m, res_asso) } } ~; print $RCMD "res_asso = res_asso[order(res_asso[, \"Trait\"], res_asso[, \"Chr\"], res_asso[, \"Pos\"]), ]\n"; print $RCMD "write.table(res_asso, '$out.res_asso', sep='\t', dec='.', quote=F, col.names=T, row.names=F)\n"; close($RCMD); system("$RSCRIPT_EXE --vanilla rscript");