get.vgu.matrix: Get paired v gene heavy chain and light chain matrix on...

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

Get paired v gene heavy chain and light chain matrix on clonotype level. A v gene usage pheatmap can be obtain by p<-pheatmap::pheatmap(vgu_matrix,show_colnames= T, main = "V Gene Usage"), where the vgu_matrix is the output of this function.

Description

Get paired v gene heavy chain and light chain matrix on clonotype level. A v gene usage pheatmap can be obtain by p<-pheatmap::pheatmap(vgu_matrix,show_colnames= T, main = "V Gene Usage"), where the vgu_matrix is the output of this function.

Usage

get.vgu.matrix(all.contig.annotations, level)

Arguments

all.contig.annotations	The dataframe "all_contig_annotation" from simulation output.
level	Can be "clone" or "cell". If "clone", the function will return paired v gene usage matrix on clonotype level. Otherwise it will return on cell level.

Value

a paired v gene heavy chain and light chain matrix on clonotype level.

Platypus documentation built on Aug. 15, 2022, 9:08 a.m.