readIndrop: Import indRop processed data

In caleblareau/indRop: Package for indrops functionality

Description

readIndrop takes a (vector of) file-path(s) that point to .tsv files that were the output of indrops pre-processing pipeline (python package).

Usage

readIndrop(paths, whichFile = FALSE)

## S4 method for signature 'character'
readIndrop(paths, whichFile = FALSE)

Arguments

paths	File paths (one or more) to .tsv files generated by indrops analyses
whichFile	= FALSE Vector that corresponds to which files each cell came from

Value

Minimally, a sparse matrix that can be used for Seurat. May be contained inside an S3 object if other parameters are set to TRUE

Examples

file1 <- paste(system.file("extdata", package = "indRop"),
"small1.counts.tsv", sep = "/")
file2 <- paste(system.file("extdata", package = "indRop"),
"small2.counts.tsv", sep = "/")
dat <- readIndrop(c(file1,file2))
# now make a Seurat object
# library(Seurat)
# seuratObject <- new("seurat", raw.data = dat) 

caleblareau/indRop documentation built on May 29, 2019, 1:17 p.m.