load_expdata: loads expression data in GxS format, with one row per gene &...

In hammerlab/rinfino: R-friendly client to run infino (http://github.com/hammerlab/infino)

Description

loads expression data in GxS format, with one row per gene & one column per sample returns a tbl_df also in GxS format, with sample-batch-assignment in attr 'sampleinfo'

Usage

load_expdata(path, gene_col = "Gene_symbol", data_loader = readr::read_tsv,
  batch = 1, filter = NULL, trans = NULL, ...)

Arguments

path	(chr) path to expression matrix
gene_col	(chr) name of column containing gene symbol
data_loader	(function) function to use when loading data
batch	(chr) optional description to give this batch
...	extra args to data_loader
expression_filter	(dbl) optional value by which to filter expression (if NULL, no filter)

Value

tbl_df containing expression data, with columns '_SAMPLE_ID' and '_BATCH'

Note

Expects data in format prepared by prep_gene_expression_matrix.R

Genes are filtered to remove those with 0 expression across all samples these can be filled in with 0 if expressed in at least one batch on combination

hammerlab/rinfino documentation built on May 27, 2019, 8:45 a.m.