cumfrac_rpc: Cumulative fraction of reads per cell barcode

In argschwind/dropseqr: Utilities for Drop-seq data processing

Description

Calculate cumulative fraction of reads per detected cell barcode. The cumulative fraction can be plotted to estimate the number of sequenced cells by identifying the "knee" of the distribution. For further details on selection of cells, see the Drop-seq alignment cookbook provided by the McCarroll lab. This function is implemented in plot_cumfrac_rpc and is only required when an alternative plot or analysis of the cumulative fraction is needed.

Usage

cumfrac_rpc(read_counts)

Arguments

read_counts

A data.frame containing the number of reads per cell barcode. Should consist of two columns, whereas the number of reads must in the first and the barcode identity in the second column. This is typically produced by running BAMTagHistogram from Drop-seq tools.

Value

A data.frame containing the original data in read_counts with an added column containing the cumulative fraction.

Examples

library(dropseqr)

# load example dataset
data(reads_per_cell_barcode)

# calculate cumulative fraction
cf <- cumfrac_rpc(reads_per_cell_barcode)

argschwind/dropseqr documentation built on May 23, 2019, 4:24 p.m.