read_tome_gene_data: Read Gene Expression Data from a tome file

In AllenInstitute/scrattch.io: scrattch File Input/Output Handling

Description

Read Gene Expression Data from a tome file

Usage

read_tome_gene_data(tome, genes = NULL, regions = "exon",
  units = "counts", transform = "none", format = "data.frame")

Arguments

tome	tome file to read. Required.
genes	A vector of gene names to read. If NULL, will read all genes.
regions	The gene regions to use. Can be "exon", "intron", or "both". Default = "exon".
units	The type of values to return. Can be "counts" or "cpm". Default = "counts".
transform	Transformation to apply to values. Can be "none", "log", "log2", "log10". Log transforms will add 1 to values before transformation. Default = "none".
format	The format of the output. Can be "data.frame", "matrix", or "dgcMatrix" (sparse matrix). Default is "data.frame".

Value

A data.frame with sample_name as the first column and each subsequent column containing gene expression values and named for the genes; Or a matrix with columns as genes and rows as samples.

AllenInstitute/scrattch.io documentation built on Nov. 17, 2021, 10:06 a.m.