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39 lines
981 B
R
39 lines
981 B
R
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# This script reads data from GTEx and transforms it into various formats for
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# further analysis. Note that this requires very good computational resources
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# and especially a lot of RAM because of the size of the data.
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library(data.table)
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library(here)
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i_am("scripts/input.R")
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# Source: https://storage.googleapis.com/gtex_analysis_v8/rna_seq_data/
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# GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_tpm.gct.gz
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# The file has been edited removing the lines above the column headers.
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data_wide_samples <- fread(here("scripts", "input", "gtex.tsv.gz"))
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setnames(
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data_wide_samples,
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c("Name", "Description"),
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c("gene", "hgnc_symbol")
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)
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data_long <- melt(
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data_wide_samples,
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id.vars = c("gene", "hgnc_symbol"),
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variable.name = "sample",
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value.name = "expression",
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variable.factor = FALSE
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)
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fwrite(
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data_wide_samples,
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file = here(
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"scripts",
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"input",
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"data_wide_samples.csv"
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)
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)
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fwrite(data_long, file = here("scripts", "input", "data_long.csv"))
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