Hair Follicle.R

# R script to download selected samples
# Copy code and run on a local machine to initiate download

# Check for dependencies and install if missing
packages <- c("rhdf5")
if (length(setdiff(packages, rownames(installed.packages()))) > 0) {
    print("Install required packages")
    source("https://bioconductor.org/biocLite.R")
    biocLite("rhdf5")
}
library("rhdf5")
library("tools")

destination_file = "human_matrix_download.h5"
extracted_expression_file = "Hair Follicle_expression_matrix.tsv"
url = "https://s3.amazonaws.com/mssm-seq-matrix/human_matrix.h5"

# Check if gene expression file was already downloaded and check integrity, if not in current directory download file form repository
if(!file.exists(destination_file)){
    print("Downloading compressed gene expression matrix.")
    download.file(url, destination_file, quiet = FALSE)
}

# Selected samples to be extracted
samp = c("GSM2072459","GSM2072458","GSM2703811","GSM2703812","GSM2703813","GSM2703814","GSM2703815","GSM2703816","GSM3717034","GSM3717035","GSM3717036","GSM3717037","GSM3717038","GSM3731086","GSM3731087","GSM3731088","GSM3731089","GSM3731090","GSM3731091","GSM3731092","GSM3731093","GSM3731094","")

# Retrieve information from compressed data
samples = h5read(destination_file, "meta/Sample_geo_accession")
tissue = h5read(destination_file, "meta/Sample_source_name_ch1")
genes = h5read(destination_file, "meta/genes")

# Identify columns to be extracted
sample_locations = which(samples %in% samp)

# extract gene expression from compressed data
expression = h5read(destination_file, "data/expression", index=list(1:length(genes), sample_locations))
H5close()
rownames(expression) = genes
colnames(expression) = samples[sample_locations]

# Print file
write.table(expression, file=extracted_expression_file, sep="\t", quote=FALSE)
print(paste0("Expression file was created at ", getwd(), "/", extracted_expression_file))