readCells: Load all experiment data into R

In joeburns06/hocuspocus: A Suite of Single-Cell RNA-Seq Analysis Tools Built for Dummy Biologists

Description

Takes separate .txt files containing assay, pheno, feature, and experiment data and combines them into a single ExpressionSet object (uses Bioconductor ExpressionSet class format).

Usage

readCells(assay, pheno, feature, experiment, color)

Arguments

assay	Character string specifying the path and filename of a tab-delimited .txt file containing a matrix of expression values (e.g. counts, FPKMs, TPMs, etc.) with cells in columns and genes in rows. Be sure to include cell and gene names as header and row names!
pheno	Character string specifying the path and filename tab-delimited .txt file containing information about the cells in separate columns. Be sure that the row names in this file match the column names in assayData (can be a subset)
feature	Character string specifying the path and filename of a tab-delimited .txt file containing information about the genes in separate columns. Be sure that the row names in this file match the row names in assayData (can be a subset)
experiment	Character string specifying the path and filename of a tab-delimited .txt file containing additional information about all the column headers in the phenoData file in separate columns. Be sure that the row names in this file match the column headers in the phenoData file.

Value

ExpressionSet object containg matrix of expression values, phenoData, assayData, and experimentData.

joeburns06/hocuspocus documentation built on May 19, 2019, 2:59 p.m.