Output Handling

Read sample data across a set of tomes that share the same genes

1 2	read_shelf_sample_data(tomes, samples, regions = "exon", units = "counts", transform = "none", format = "data.frame")

`tomes`	a character vector of tome file locations
`samples`	A vector of sample names to read. Required.
`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".

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.