VDJ_GEX_stats: Standalone VDJ and GEX statistics.

In Platypus: Single-Cell Immune Repertoire and Gene Expression Analysis

Standalone VDJ and GEX statistics.

Description

Gives stats on number and quality of reads. This function is integrated into the VDJ_GEX_matrix. Before running, please check list element [[3]] of VDJ_GEX_matrix output for already generated statistics.

Usage

VDJ_GEX_stats(
  VDJ.out.directory,
  GEX.out.directory,
  sample.names,
  metrics10x,
  save.csv,
  filename
)

Arguments

VDJ.out.directory	List of paths with each element containing the path to the output of cellranger VDJ runs. This pipeline assumes that the output file names have not been changed from the default 10x settings in the /outs/ folder. This is compatible with B and T cell repertoires (both separately and simultaneously).
GEX.out.directory	OPTIONAL list of paths with each element containing the path to the output of cellranger GEX runs. This pipeline assumes that the output file names have not been changed from the default 10x settings in the /outs/ folder. This is compatible with B and T cell repertoires (both separately and simultaneously).
sample.names	OPTIONAL: an array of the same length as the input VDJ.out.directory list with custom names for each sample. If not provided samples will be numbered by processing order
metrics10x	Whether to append metrics_summary.csv information provided by Cellranger for both VDJ and GEX. Defaults to T
save.csv	Boolean. Defaults to TRUE. Whether to directly save the resuts as a comma delimited .csv file in the current working directory.
filename	Character ending in .csv. Filename to save .csv as.

Value

returns a single matrix where the rows are individual cells and the columns are repertoire features.

Examples

try({
stats <- VDJ_GEX_stats(VDJ.out.directory = VDJ.out.directory.list
,GEX.out.directory = GEX.out.directory.list,sample.names = c(1:4)
,metrics10x = TRUE,save.csv = FALSE)
})

Platypus documentation built on Oct. 18, 2024, 5:08 p.m.