bc_subset: Manages barcodes and samples in a BarcodeObj object

In wenjie1991/CellBarcode: Cellular DNA Barcode Analysis toolkit

Manages barcodes and samples in a BarcodeObj object

Description

A set of functions and operators for subsetting or joining of BarcodeObj object(s). The bc_subset, * and - are used to select barcodes or samples in a BarcodeObj object. Two BarcodeObj objects can be joined by +.

Usage

bc_subset(
  barcodeObj,
  sample = NULL,
  barcode = NULL,
  black_list = NULL,
  is_sample_quoted_exp = FALSE
)

bc_merge(barcodeObj_x, barcodeObj_y)

## S4 method for signature 'BarcodeObj'
bc_subset(
  barcodeObj,
  sample = NULL,
  barcode = NULL,
  black_list = NULL,
  is_sample_quoted_exp = FALSE
)

## S4 method for signature 'BarcodeObj,BarcodeObj'
bc_merge(barcodeObj_x, barcodeObj_y)

## S3 method for class 'BarcodeObj'
barcodeObj_x + barcodeObj_y

## S3 method for class 'BarcodeObj'
barcodeObj - black_list

## S3 method for class 'BarcodeObj'
barcodeObj * white_list

Arguments

barcodeObj	A BarcodeObj object.
sample	A character vector or integer vector or an expression (expressio not applicable for [] operator), specifying the samples in the subsets. When the value is an expression, the columns in the metadata can be used as a variable.
barcode	A vector of integer or string, indicating the selected barcode.
black_list	A character vector, specifying the black list with excluded barcodes.
is_sample_quoted_exp	A logical value. If TRUE, the expression in sample argument will not be evaluated before executing the function.
barcodeObj_x	A BarcodeObj object.
barcodeObj_y	A BarcodeObj object.
white_list	A character vector, giving the barcode white list.

Details

bc_subset and []: Gets samples and barcodes subset from a BarcodeObj object.

+: Combines two BarcodeObj objects. The metadata, cleanBc and messyBc slot in the BarcodeObj objects will be joined. For the metadata slot, the sample_name column, and the Full outer join (the record in either BarcodeObj object) will be performed with row names as the key. The messyBc and cleanBc from two objects are combined by rows for the same sample from two BarcodeObj objects.

-: removes barcodes in the black_list.

*: selects barcodes in the white_list.

Value

A BarcodeObj object.

Examples

data(bc_obj)

bc_obj

# Select barcodes
bc_subset(bc_obj, barcode = c("AACCTT", "AACCTT"))
bc_obj[c("AGAG", "AAAG"), ]

# Select samples by metadata
bc_meta(bc_obj)$phenotype <- c("l", "b")
bc_meta(bc_obj)
bc_subset(bc_obj, phenotype == "l")

# Select samples by sample name
bc_obj[, "test1"]
bc_obj[, c("test1", "test2")]
bc_subset(bc_obj, sample = "test1", barcode = c("AACCTT", "AACCTT"))

# Apply barcode blacklist
bc_subset(
bc_obj,
    sample = c("test1", "test2"),
    barcode = c("AACCTT"))

# Join two samples with different barcode sets
bc_obj["AGAG", "test1"] + bc_obj["AAAG", "test2"]

# Join two samples with overlap barcodes
bc_obj_join <- bc_obj["AGAG", "test1"] + bc_obj["AGAG", "test2"]
bc_obj_join
# The same barcode will be removed after applying bc_cure_depth()
bc_cure_depth(bc_obj_join)

# Remove barcodes
bc_obj
bc_obj - "AAAG"

# Select barcodes in a whitelist
bc_obj
bc_obj * "AAAG"
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wenjie1991/CellBarcode documentation built on Aug. 10, 2024, 11:02 a.m.