Process GTEx expression data — process_GTEx_gene

GTEx gene reads file is processed to obtain the average normalized gene expression in a tissue

Usage

process_GTEx_gene_reads(
  geneReads = NULL,
  GTEx_annot = NULL,
  tissue = NULL,
  id_type = c("gene_id", "symbol"),
  nrows = -1,
  norm.type = "LogNormalize",
  ...
)

Arguments

geneReads: GTEx gene reads "gct" file, e.g. "GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_reads.gct"
GTEx_annot: GTEx Sample annotation file, e.g. "GTEx_Analysis_v8_Annotations_SampleAttributesDS.txt"
tissue: tissue name, see param "SMTS" in annotation
id_type: whether the output should be specified as gene_id or symbol
nrows: limit the read to the top nrows. Useful for testing.
norm.type: Method for normalization. See Seurat::NormalizeData.
...: further arguments passed to functin Seurat::NormalizeData.

Value

average normalized gene expression values