AppendCiteSeq: Read/Append CITE-seq/ADT data to a Seurat Object

In bimberlabinternal/CellMembrane: A package with high-level wrappers and pipelines for single-cell RNA-seq tools

Read/Append CITE-seq/ADT data to a Seurat Object

Description

Read/Append CITE-seq/ADT data to a Seurat Object

Usage

AppendCiteSeq(
  seuratObj,
  unfilteredMatrixDir,
  normalizeMethod = "dsb",
  datasetId = NULL,
  assayName = "ADT",
  featureMetadata = NULL,
  adtWhitelist = NULL,
  minRowSum = NULL,
  failIfAdtsInWhitelistNotFound = TRUE,
  aggregateBarcodeFile = NULL
)

Arguments

seuratObj	The seurat object where data will be added.
unfilteredMatrixDir	The directory holding raw count data, generally the raw_feature_bc_matrix from the cellranger outs folder
normalizeMethod	The method for normalization. If NULL, normalization will be skipped.
datasetId	If the seurat object includes cells from multiple datasets, and/or if the barcodes were prefixed with a dataset id, This will be used as a prefix for barcodes, and stored in metadata. Also used as the project name for the Seurat object.
assayName	The name of the assay to store ADT data.
featureMetadata	If is common for the raw barcode to use non-human friendly names (like TotalSeq-C-XXXX). This is an optional dataframe that can be used to override that, and also provide other feature metadata. This dataframe must have rownames that match the rownames of the saved matrix. If this dataframe has the column 'name', this will be used to replace the original rownames on the ADT assay.
adtWhitelist	An optional whitelist of ADT names (matching the raw names from the matrix). If provided, the matrix will be subset to just these features
minRowSum	If provided, any ADTs (rows) with rowSum below this value will be dropped.
failIfAdtsInWhitelistNotFound	If an adtWhitelist is provided and this is TRUE, an error will be thrown if any of these features are missing in the input matrix
aggregateBarcodeFile	Optional. This is the cellranger output, in antibody_analysis/aggregate_barcodes.csv, which contains barcodes marked as aggregates. These are dropped.

bimberlabinternal/CellMembrane documentation built on Oct. 16, 2024, 6:53 a.m.