Subset a TIRTLseqDataSet object

The filter_dataset() function is used to select a subset of samples from a loaded TIRTLseq dataset and create a new dataset object.

Usage

filter_dataset(data, samples)

Arguments

data

a TIRTLseqDataSet object created by load_tirtlseq()

samples

the selected samples. Either 1) a numeric vector of indices, 2) a character vector of sample names, or 3) a character vector of metadata conditions where each entry is of the form "column==value".

Value

A dataset object similar to that created by load_tirtlseq(), but with only the selected samples.

Details

The function accepts 1) a numeric vector of indices, 2) a character vector of sample names, or 3) a character vector of metadata conditions where each entry is of the form "column==value".

In the third case, c("cell_type==cd4", "timepoint==tp2") would, for example, select samples whose cell_type is cd4 and whose timepoint is tp2 in the sample metadata.

See also

Other data_wrangling: add_metadata(), reorder_samples()

Examples

folder = system.file("extdata/SJTRC_TIRTL_seq_longitudinal",
  package = "TIRTLtools")
sjtrc = load_tirtlseq(folder,
  meta_columns = c("marker", "timepoint", "version"), sep = "_",
  chain = "paired", verbose = FALSE)
p2 = filter_dataset(sjtrc, 1:3) ### by indices
p3 = filter_dataset(sjtrc, c("cd8_tp1_v2", "cd8_tp2_v2", "cd8_tp3_v2")) ### by sample names
p4 = filter_dataset(sjtrc, "marker==cd4") ### by sample metadata condition
p5 = filter_dataset(sjtrc, c("marker==cd4", "timepoint==tp2")) ### by multiple sample metadata conditions