Skip to contents

Find sample-level Cell Ranger output folders

TS_find_cellranger_samples.Rd

Recursively searches a project folder for Cell Ranger matrix directories and infers the corresponding sample names. The function is designed for common cellranger multi layouts such as outs/per_sample_outs/<sample> and for project folders organised as project/<sample>/cellranger_outs.

The filtered gene expression matrix is detected at sample level. V(D)J directories are detected at run level, for example outs/vdj_b and outs/vdj_t, because cellranger multi stores the unfiltered all_contig* files there rather than in per_sample_outs/<sample>.

Usage

TS_find_cellranger_samples(
  input_dir,
  sample_regex = NULL,
  matrix_dir_names = c("filtered_feature_bc_matrix", "sample_filtered_feature_bc_matrix"),
  vdj_dir_names = c("vdj_b", "vdj_t")
)

Arguments

input_dir

Character scalar. Project or Cell Ranger output directory to search.

sample_regex

Optional regular expression used to extract sample names from matrix directory paths. If the regular expression contains a capture group, the first captured group is used; otherwise the full match is used.

matrix_dir_names

Character vector of matrix directory names to search for. Defaults to Cell Ranger's filtered_feature_bc_matrix and sample_filtered_feature_bc_matrix.

vdj_dir_names

Character vector of V(D)J directory names to detect.

Value

A tibble with one row per detected sample matrix and columns sample_id, sample_root, outs_dir, matrix_dir, vdj_b_dir, vdj_t_dir, and detection_note.

Examples

project <- file.path(tempdir(), "cellranger_project")
matrix_dir <- file.path(project, "sampleA", "cellranger_outs", "filtered_feature_bc_matrix")
dir.create(matrix_dir, recursive = TRUE, showWarnings = FALSE)
file.create(file.path(matrix_dir, c("barcodes.tsv.gz", "features.tsv.gz", "matrix.mtx.gz")))
#> [1] TRUE TRUE TRUE

TS_find_cellranger_samples(project)
#> # A tibble: 1 × 7
#>   sample_id sample_root   outs_dir matrix_dir vdj_b_dir vdj_t_dir detection_note
#>   <chr>     <chr>         <chr>    <chr>      <chr>     <chr>     <chr>         
#> 1 sampleA   /tmp/RtmpBku… /tmp/Rt… /tmp/Rtmp… NA        NA        cellranger_ou…