VGM_build: Function to obtain the VGM object by integrating the VDJ and...

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

Function to obtain the VGM object by integrating the VDJ and GEX/Seurat objects

Description

Takes as input a VDJ data frame (as obtained from the VDJ function in Platypus) and a Seurat object. Outputs an integrated VGM object (a list with the first element - the VDJ object; second element - the Seurat object). Integration involves matching by barcodes and adding all features from one object to the other and vice-versa. Authors: Tudor-Stefan Cotet, Victor Kreiner

Usage

VGM_build(VDJ, GEX, merge.by, additional.dataframes, columns.to.transfer)

Arguments

VDJ	VDJ data frame, obtained from the Platypus VDJ() function
GEX	Seurat object for the single-cell immune receptor repertoire analysis.
merge.by	string - the column name to match both objects/dataframes by. Should be present in both objects (Seurat object meta.data and VDJ dataframe). Defaults to "barcode."
additional.dataframes	vector of data frames - additional dataframes to be matched/merged to the VDJ and GEX. Will be matched by the column denoted in the merge.by parameter (should be present in the VDJ and all subsequent dataframes).
columns.to.transfer	string or vector of strings - columns that should be transferred/appended across all objects (matched by the merge.by parameter). Defaults to "all" - all unique columns from GEX not present in VDJ and vice-versa.

Value

An output VGM object: a list with the first element - the VDJ object; second element - the GEX/Seurat object. Additonal elements are appended to the list if additional.dataframes is not null.

Examples

try({
small_vgm <- VGM_build(
VDJ = small_vgm[[1]],
GEX = small_vgm[[2]],
columns.to.transfer = 'all') #transfer all new columns
})

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