Filter V(D)J data in object — filter

Remove V(D)J data for chains/cells that do not satisfy the provided condition

Usage

filter_vdj(
  input,
  filt,
  data_cols = NULL,
  clonotype_col = "clonotype_id",
  sep = global$sep,
  per_chain = TRUE
)

Arguments

input: Single cell object or data.frame containing V(D)J data. If a data.frame is provided, cell barcodes should be stored as row names.
filt: Condition to use for filtering V(D)J data. To allow for filtering of per-chain V(D)J data, the data for each cell is converted into a vector, e.g. 'IGH;IGK' is equivalent to c('IGH', 'IGK'). This allows R vector operations to be performed on the per-chain values. The filtering condition must return TRUE/FALSE for each chain or a single TRUE/FALSE for each cell. Data can be filtered based on cell barcodes by referring to the '.cell_id' column.
data_cols: meta.data columns containing V(D)J data to use for filtering. If NULL, V(D)J data are automatically selected by identifying columns that have NAs in the same rows as clonotype_col.
clonotype_col: meta.data column containing clonotype IDs. This column is used to determine which columns contain V(D)J data.
sep: Separator used for storing per cell V(D)J data.
per_chain: If TRUE per-chain data will be parsed so values for individual chains can be filtered, if FALSE values will be filtered as is.

Value

Object with filtered meta.data

Examples

# Only include V(D)J data for productive chains
res <- filter_vdj(vdj_sce, productive)

# Only include V(D)J data for cells with paired chains
res <- filter_vdj(vdj_sce, paired)

# Only include V(D)J data for cells with at least one heavy and one light
# chain
res <- filter_vdj(
  vdj_sce,
  "IGH" %in% chains && any(c("IGK", "IGL") %in% chains)
)

# Only include V(D)J data for cells that have an IGH, IGK, and IGL chain
res <- filter_vdj(
  vdj_sce,
  all(c("IGH", "IGK", "IGL") %in% chains)
)

# Only include V(D)J data for heavy chains
res <- filter_vdj(vdj_sce, chains == "IGH")

# Remove chains that only have 1 UMI for support
res <- filter_vdj(vdj_sce, umis > 1)

# Filter based on cell barcode
res <- filter_vdj(vdj_sce, .cell_id == "1_ACGGAGACATGCTGGC-1")