readVDJcontigs: Load 10X CellRanger V(D)J data

In kstreet13/VDJdive: Analysis Tools for 10X V(D)J Data

Load 10X CellRanger V(D)J data

Description

Creates a SplitDataFrameList (see DataFrameList) from a character vector of directory names corresponding to the output of the CellRanger V(D)J pipeline.

Usage

readVDJcontigs(samples, ...)

## S4 method for signature 'character'
readVDJcontigs(samples, sample.names = names(samples))

Arguments

samples	A character vector containing one or more directory names, each corresponding to a 10X sample. Each directory should contain a file named filtered_contig_annotations.csv.
...	additional arguments.
sample.names	A character vector of length equal to samples containing the sample names to store in the output object. If NULL, the basenames of each directory will be used.

Details

The resulting list of DataFrames contains all the data in filtered_contig_annotations.csv, split by cell barcode. Note that the index of each sample in samples is concatenated to the cell barcodes, so that cells from different samples cannot have identical barcodes.

Value

A SplitDataFrameList object containing data on all contigs, grouped by cell barcode.

Examples

# write the example data to a temporary directory
example(writeVDJcontigs)
# specify sample locations and read in data
samples <- file.path(loc, c('sample1','sample2'))
contigs <- readVDJcontigs(samples)

kstreet13/VDJdive documentation built on May 27, 2023, 8:08 a.m.