mirror of
https://github.com/johrpan/ubigen.git
synced 2025-10-26 19:57:24 +01:00
Elias Projahn
cc17c13888
This commit also changes the way the standard deviation and mean expression are computed in general. Now, samples where the gene is not expressed at all are excluded before the computation.
38 lines
987 B
R
38 lines
987 B
R
# 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.gz"
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)
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)
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fwrite(data_long, file = here("scripts", "input", "data_long.csv.gz"))
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