Load samples into a Seurat object — LoadSeuratAndPerformQC • biopipen.utils

Cell QC will be performed, either per-sample or on the whole object

Usage

LoadSeuratAndPerformQC(
  meta,
  samples = NULL,
  per_sample_qc = FALSE,
  cell_qc = NULL,
  gene_qc = NULL,
  tmpdir = NULL,
  log = NULL,
  cache = NULL
)

Arguments

meta

Metadata of the samples Required columns: Sample, RNAData. The RNAData column should contain the path to the 10X data, either a directory or a file If the path is a directory, the function will look for barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz. The directory should be loaded by Seurat::Read10X. Sometimes, there may be prefix in the file names, e.g. "'prefix'.barcodes.tsv.gz", which is also supported. If the path is a file, it should be a h5 file that can be loaded by Seurat::Read10X_h5

samples

Samples to load. If NULL, all samples will be loaded

per_sample_qc

Whether to perform per-sample cell QC

cell_qc

Cell QC criteria

gene_qc

Gene QC criteria A list containing the following fields:

min_cells: Minimum number of cells a gene should be expressed in to be kept
excludes: A string or strings to exclude certain genes. Regular expressions are supported. Multiple strings can also be separated by commas in a single string.

tmpdir

Temporary directory to store intermediate files when there are prefix in the file names

log

Logger

cache

Directory to cache the results. Set to FALSE to disable caching

Value

A Seurat object. In slot misc, there are two fields: cell_qc_df and gene_qc, a list of gene QC results

Examples

# \donttest{
datadir <- system.file("extdata", "scrna", package = "biopipen.utils")
meta <- data.frame(
    Sample = c("Sample1", "Sample2"),
    RNAData = c(
        file.path(datadir, "Sample1"),
        file.path(datadir, "Sample2")
    )
)
obj <- LoadSeuratAndPerformQC(meta, cache = FALSE, gene_qc = list(min_cells = 3))
#> INFO    [2025-01-03 21:07:38] Loading each sample ...
#> INFO    [2025-01-03 21:07:38] - Loading sample Sample1 ...
#> INFO    [2025-01-03 21:07:38] - Loading sample Sample2 ...
#> INFO    [2025-01-03 21:07:38] Merging samples ...
#> INFO    [2025-01-03 21:07:39] Performing cell QC ...
#> INFO    [2025-01-03 21:07:39] Performing gene QC ...
head(obj@misc$cell_qc_df)
#>                  Sample nFeature_RNA nCount_RNA percent.mt percent.ribo
#> Sample1_TEINH_1 Sample1         1153       2196          0            0
#> Sample1_TEINH_2 Sample1         1219       2560          0            0
#> Sample1_TEINH_3 Sample1          981       1784          0            0
#> Sample1_TEINH_4 Sample1         1159       2159          0            0
#> Sample1_TEINH_5 Sample1         1111       1841          0            0
#> Sample1_TEINH_6 Sample1          766       1236          0            0
#>                 percent.hb percent.plat  .QC
#> Sample1_TEINH_1          0            0 TRUE
#> Sample1_TEINH_2          0            0 TRUE
#> Sample1_TEINH_3          0            0 TRUE
#> Sample1_TEINH_4          0            0 TRUE
#> Sample1_TEINH_5          0            0 TRUE
#> Sample1_TEINH_6          0            0 TRUE
print(obj@misc$gene_qc)
#> $before
#> [1] 3636
#> 
#> $criteria
#> $criteria$min_cells
#> [1] 3
#> 
#> 
#> $ncells
#>       Sample         feature ncells
#> 79   Sample1 ENSG00000145708      2
#> 182  Sample1 ENSG00000100097      4
#> 383  Sample1 ENSG00000225968      3
#> 398  Sample1 ENSG00000211445      0
#> 703  Sample1 ENSG00000152822      1
#> 749  Sample1 ENSG00000277586      5
#> 996  Sample1 ENSG00000143479      4
#> 1054 Sample1 ENSG00000072657      2
#> 1547 Sample1 ENSG00000101463      0
#> 1554 Sample1 ENSG00000079102      0
#> 1558 Sample1 ENSG00000172137      2
#> 1560 Sample1 ENSG00000188803      2
#> 1684 Sample1 ENSG00000183773      2
#> 1703 Sample1 ENSG00000150556      3
#> 1785 Sample1 ENSG00000101327      1
#> 1942 Sample1 ENSG00000106852      2
#> 2011 Sample1 ENSG00000006128      2
#> 2040 Sample1 ENSG00000130751      1
#> 2126 Sample1 ENSG00000082074      2
#> 2279 Sample1 ENSG00000188647      1
#> 2316 Sample1 ENSG00000166407      0
#> 2340 Sample1 ENSG00000118733      3
#> 2343 Sample1 ENSG00000151693      3
#> 2446 Sample1 ENSG00000166863      2
#> 2453 Sample1 ENSG00000133101      2
#> 2543 Sample1 ENSG00000185513      1
#> 2561 Sample1 ENSG00000123096      2
#> 2881 Sample1 ENSG00000162631      4
#> 2982 Sample1 ENSG00000163873      2
#> 3028 Sample1 ENSG00000112893      2
#> 3057 Sample1 ENSG00000262655      1
#> 3085 Sample1 ENSG00000164326      0
#> 3172 Sample1 ENSG00000090006      5
#> 3188 Sample1 ENSG00000181234      1
#> 3202 Sample1 ENSG00000113657      4
#> 3386 Sample1 ENSG00000168546      2
#> 3506 Sample1 ENSG00000189409      2
#> 3510 Sample1 ENSG00000165973      2
#> 3594 Sample1 ENSG00000054803      0
#> 3715 Sample2 ENSG00000145708      5
#> 3818 Sample2 ENSG00000100097      2
#> 4019 Sample2 ENSG00000225968      0
#> 4034 Sample2 ENSG00000211445      3
#> 4339 Sample2 ENSG00000152822      3
#> 4385 Sample2 ENSG00000277586      2
#> 4632 Sample2 ENSG00000143479      1
#> 4690 Sample2 ENSG00000072657      3
#> 5183 Sample2 ENSG00000101463      0
#> 5190 Sample2 ENSG00000079102      1
#> 5194 Sample2 ENSG00000172137      1
#> 5196 Sample2 ENSG00000188803      0
#> 5320 Sample2 ENSG00000183773      4
#> 5339 Sample2 ENSG00000150556      2
#> 5421 Sample2 ENSG00000101327      0
#> 5578 Sample2 ENSG00000106852      2
#> 5647 Sample2 ENSG00000006128      1
#> 5676 Sample2 ENSG00000130751      4
#> 5762 Sample2 ENSG00000082074      5
#> 5915 Sample2 ENSG00000188647      3
#> 5952 Sample2 ENSG00000166407      0
#> 5976 Sample2 ENSG00000118733      1
#> 5979 Sample2 ENSG00000151693      2
#> 6082 Sample2 ENSG00000166863      1
#> 6089 Sample2 ENSG00000133101      2
#> 6179 Sample2 ENSG00000185513      5
#> 6197 Sample2 ENSG00000123096      5
#> 6517 Sample2 ENSG00000162631      1
#> 6618 Sample2 ENSG00000163873      1
#> 6664 Sample2 ENSG00000112893      2
#> 6693 Sample2 ENSG00000262655      0
#> 6721 Sample2 ENSG00000164326      0
#> 6808 Sample2 ENSG00000090006      2
#> 6824 Sample2 ENSG00000181234      2
#> 6838 Sample2 ENSG00000113657      2
#> 7022 Sample2 ENSG00000168546      3
#> 7142 Sample2 ENSG00000189409      1
#> 7146 Sample2 ENSG00000165973      2
#> 7230 Sample2 ENSG00000054803      1
#> 
#> $after
#> [1] 3597
#> 
# }