run_estimate: Run estimate on expression data

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

Description

Run estimate on expression data

Usage

run_estimate(expdf, tmpdir = tempdir(), input_filename = file.path(tmpdir,
  "estimate_input.gct"), output_filename = file.path(tmpdir,
  "estimate_output.gct"), trans = NULL, filter_fun = NULL)

Arguments

expdf	(tbl_df or data.frame) GxS expression data with sampleinfo attr
tmpdir	(chr) optional path to working directory in which to execute estimate
input_filename	(chr) optional full path to input file for estimate
output_filename	(chr) optional full path to output file for estimate (raw, unprocessed)
trans	(function) optional transform to apply to expression data prior to computing ESTIMATE
filter_fun	(function) optional filter to apply to expression data, based on row-wise values

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