PlatypusDB_VGM_to_AIRR: Platypus V3 VGM to AIRR compatibility function

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

Platypus V3 VGM to AIRR compatibility function

Description

Exports AIRR compatible tables supplemented with VDJ and GEX information from the Platypus VGM object and the cellranger output airr_rearrangements.tsv

Usage

PlatypusDB_VGM_to_AIRR(
  VGM,
  VDJ.features.to.append,
  GEX.features.to.append,
  airr.rearrangements,
  airr.integrate
)

Arguments

VGM	Output object of the VDJ_GEX_matrix function generated with VDJ.combine = T, GEX.combine = T (to merge all samples) and integrate.VDJ.to.GEX = T (to integrate VDJ and GEX data)
VDJ.features.to.append	Character vector. Defaults to "none". Can be either "all" or column names of the VGM VDJ matrix (VGM[[1]]) to append to the AIRR compatible table.
GEX.features.to.append	Character vector. Defaults to "none". Can be either "all" or GEX metadata column names or Gene names of the VGM GEX object (VGM[[2]])(passed to Seurat::FetchData()) to append to the AIRR compatible table. For a list of available features run: names(VGM[[2]]@meta.data) and rownames(VGM[[2]])
airr.rearrangements	Source of the airr_rearrangements.tsv file as generated by Cellranger. There are 3 available input options: 1. R list object from Platypus_DB_load_from_disk or Platypus_DB_fetch / 2. List with local paths to airr_rearrangements.tsv / 3. List of airr_rearrangements.tsv loaded in as R objects within the current R enviroment. ! Order of input list must be identical to that of sample_ids in the VGM ! If not provided or set to "none" CIGAR strings in output will be empty.
airr.integrate	Boolean. Defaults to TRUE, whether to integrate output AIRR tables

Value

A list of length of samples in VGM containing a AIRR-compatible dataframe for each sample if airr.integrate = F or a single dataframe if airr.integrate = T ! Cave the format: VGM object => 1 cell = 1 row; AIRR table 1 cell = as many rows as VDJ and VJ chains available for that cell. GEX cell-level information is attached to all rows containing a chain of that cell.

Examples

try({
airr.list.out <- PlatypusDB_VGM_to_AIRR(VGM = VGM
, VDJ.features.to.append = c("VDJ_cdr3s_aa")
, GEX.features.to.append = c("CTLA4", "TOX"), airr.rearrangements = Data.in)

airr.list.out <- PlatypusDB_VGM_to_AIRR(VGM = VGM
, VDJ.features.to.append = c("VDJ_cdr3s_aa")
, GEX.features.to.append = c("CTLA4", "TOX"),
airr.rearrangements =list("~/path_to/s1/airr.rearrangement.tsv"
,"~/path_to/s2/airr_rearrangement.tsv"))

airr.list.out <- PlatypusDB_VGM_to_AIRR(VGM = VGM
, VDJ.features.to.append = c("VDJ_cdr3s_aa")
, GEX.features.to.append = c("CTLA4", "TOX"),
airr.rearrangements = list(airr_rearrangements.s1, airr_rearrangements_2))

VDJ.out.directory.list <- list()
VDJ.out.directory.list[[1]] <- c("~/cellrangerVDJ/s1")
VDJ.out.directory.list[[2]] <- c("~/cellrangerVDJ/s2")

GEX.out.directory.list <- list()
GEX.out.directory.list[[1]] <- c("~/cellrangerGEX/s1")
GEX.out.directory.list[[2]] <- c("~/cellrangerGEX/s2")
VGM <- VDJ_GEX_matrix(VDJ.out.directory.list = VDJ.out.directory.list,
GEX.out.directory.list = GEX.out.directory.list,
GEX.integrate = TRUE, VDJ.combine = TRUE, integrate.GEX.to.VDJ = TRUE
, integrate.VDJ.to.GEX = TRUE,
get.VDJ.stats = FALSE, trim.and.align = FALSE)
airr.list.out <- PlatypusDB_VGM_to_AIRR(VGM = VGM,
VDJ.features.to.append = c("VDJ_sequence_nt_trimmed","VJ_sequence_nt_trimmed"),
GEX.features.to.append = c("UMAP_1","UMAP_2","CTLA4", "TOX"),
airr.rearrangements = c("~/cellrangerVDJ/s1/airr_rearrangement.tsv"
,"~/cellrangerVDJ/s2/airr_rearrangement.tsv"))
})

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