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# install.packages("data.table", "dplyr") | |
library(data.table) | |
library(dplyr) | |
parseProperly <- function(x){ | |
x <- x[,-c(ncol(x)-1,ncol(x))] | |
x | |
} | |
# Read data drectly from GEO | |
m1 <- "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124167/suppl/GSE124167_FINAL_master_list_of_gene_counts_MIN.V4.txt.gz" | |
m2 <- "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124167/suppl/GSE124167_FINAL_master_list_of_gene_counts_MIN.sense.Pico.R.txt.gz" | |
m3 <- "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124167/suppl/GSE124167_FINAL_master_list_of_gene_counts_MIN.sense.Truseq.txt.gz" | |
method1 <- parseProperly(fread(m1, data.table=FALSE)) | |
method2 <- parseProperly(fread(m2, data.table=FALSE)) | |
method3 <- parseProperly(fread(m3, data.table=FALSE)) | |
# Combine into a single table | |
counts <- Reduce(function(x, y) full_join(x, y, by="id"), list(method1, method2, method3)) | |
# Replace NAs by zero | |
counts[is.na(counts)] <- 0 | |
# Move "ids" to rownames to have a ure count matrix: | |
rownames(counts) <- counts$id | |
counts$id <- NULL |
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