get_overrepresented_spikes: Find overrepresented spUMI sequences

In cziegenhain/UMIcountR: tools for spike-in UMI analysis

Find overrepresented spUMI sequences

Description

get_overrepresented_spikes is used to find the spUMIs of overrepresented molecular spikes.

Usage

get_overrepresented_spikes(dat, readcutoff = 100, nbccutoff = 5)

Arguments

dat	input data.table of loaded spUMI data. Must have BC and spikeUMI_hd2 columns.
readcutoff	maximum number of raw reads a spUMI should be observed in, Default: 100
nbccutoff	maximum number of cell barcodes a spUMI should be observed in, Default: 5

Details

Visualise filtering plots by accessing the "plots" list element of the output. over_readcutoff = spUMIs that are more abundant than the set cutoff of number of reads. over_nbcs = spUMIs that are observed in more cell barcodes than the set cutoff.

Value

returns a list of length 3, where the first list element "plots" contains descriptive plots of chosen filtering cutoffs and the list elements "over_readcutoff" and "over_nbcs" contain the spUMI identities that should be discarded.

See Also

data.table-package

Examples

## Not run: 
get_overrepresented_spikes(spikedat, readcutoff = 100, nbccutoff = 5)

## End(Not run)

cziegenhain/UMIcountR documentation built on May 30, 2022, 5:38 p.m.