alignRate: alignRate

In chris-mcginnis-ucsf/MULTI-seq: deMULTIplex is a software suite for MULTI-seq sample barcode FASTQ pre-processing and cell barcode classification.

alignRate

Description

'alignRate' computes the proportion of sample barcode reads that align with <1 mismatch to any sample barcode reference sequence.

Usage

 alignRate(readTable, cellIDs, ref) 

Arguments

readTable	Read table comprised of CellID (R1), UMI (R1), and sample barcode (R2), as generated using MULTIseq.preProcess.
cellIDs	Vector of cellIDs with which to compute the alignment rate.
ref	Vector of sample barocde sequences with which to compute the alignment rate.

Value

Vector of length cellIDs with alignment rate values (0-100) for each cell.

Author(s)

Chris McGinnis

Examples

 ar <- alignRate(readTable, cellIDs, ref) 

chris-mcginnis-ucsf/MULTI-seq documentation built on Nov. 22, 2023, 8:24 p.m.