From 6ac2193edbdf91f2adb40acf9a69b33052c05df6 Mon Sep 17 00:00:00 2001 From: Eric Harshfield Date: Mon, 18 Jun 2018 16:00:19 +0100 Subject: [PATCH] Fixed bugs in commands that install biocLite packages and subset list of proxy SNPs --- ProGeM_commands.R | 2 +- ProGeM_settings.r => ProGeM_settings.R | 0 README.md | 2 +- 3 files changed, 2 insertions(+), 2 deletions(-) rename ProGeM_settings.r => ProGeM_settings.R (100%) diff --git a/ProGeM_commands.R b/ProGeM_commands.R index 5a49471..93dfba3 100644 --- a/ProGeM_commands.R +++ b/ProGeM_commands.R @@ -27,7 +27,7 @@ proxy_data <- data.table(read.table(file = file.path(base_dir, proxy_filename), if(filtering_required == TRUE) { proxy_data <- proxy_data[proxy_data$r2 >= r2_thresh,] } -proxy_data <- proxy_data[-which(proxy_data$PROXY_rsID == proxy_data$LEAD_rsID),] +proxy_data <- proxy_data[which(proxy_data$PROXY_rsID != proxy_data$LEAD_rsID),] # add a new column containing chromsome and position information in the format: "chr_position_" (this diff --git a/ProGeM_settings.r b/ProGeM_settings.R similarity index 100% rename from ProGeM_settings.r rename to ProGeM_settings.R diff --git a/README.md b/README.md index 4487cee..9482930 100644 --- a/README.md +++ b/README.md @@ -79,7 +79,7 @@ MODIFIER_impact <- c("coding_sequence_variant", "mature_miRNA_variant", "5_prime ``` r source("https://bioconductor.org/biocLite.R") -biocLite("GenomicAlignments", "GenomicFeatures", "GenomicRanges", "biomaRt") +biocLite(c("GenomicAlignments", "GenomicFeatures", "GenomicRanges", "biomaRt")) install.packages("data.table") ```