catcheR_merge - Merge multiple samplesΒΆ

If fine-tuning is applied after catcheR_10Xcatch() and multiple samples are analyzed independently, use catcheR_merge() to aggregate the results into a single annotated matrix.

Note

If all samples were processed at once using the samples argument in catcheR_10Xcatch(), this step is done automatically and does not need to be repeated.

Run:

catcheR_merge(
    group = c("docker", "sudo"),
    folder,
    samples = 2,
    empty = TRUE
)

Arguments:

  • group: either "docker" or "sudo", depending on user permissions (see: https://docs.docker.com/engine/install/linux-postinstall/)

  • folder: path to the working directory containing the per-sample outputs

  • samples: integer, the number of samples to be merged

  • empty: boolean, whether to include cells identified as empty (from catcheR_10Xnocatch())

Example usage:

catcheR_merge(
    group = "docker",
    folder = "/20tb/ratto/catcheR/test_CM5/",
    samples = 4
)

Output:

  • A single merged silencing_matrix.csv file (and RDS version), aggregating data across all provided samples. If empty = TRUE, the merged matrix includes cells with no shRNA integration for use as negative controls.