catcheR_filtercatch - Fine-Tune iPS2-10X-seq Perturbation Assignment

Still within the same working directory used for catcheR_10Xcatch(), you can re-apply filtering with user-defined thresholds by running:

catcheR_filtercatch(
    group = c("docker", "sudo"),
    folder,
    expression.matrix,
    UMI.count,
    percentage = 15,
    ratio = 5,
    sample = 1
)

Arguments:

  • group: either “docker” or “sudo”, depending on your system permissions

  • folder: string with the working directory path

  • expression.matrix: string with the filename of the cell-by-gene count matrix (CSV format)

  • UMI.count: integer threshold for the minimum number of UMIs per UCI to be considered valid

  • percentage: integer percentage threshold for a UCI to be accepted in a cell (e.g., if percentage = 15, the UCI must account for ≥15% of all UMI in that cell)

  • ratio: integer minimum ratio of the top UMI count to the second-highest in a cell to accept the top UCI (default = 5)

  • sample: integer specifying the sample number (default = 1). Run this step separately for each sample.

Example:

catcheR_filtercatch(
    group = "docker",
    folder = "path/to/working/folder",
    expression.matrix = "filename.csv",
    UMI.count = 5,
    sample = 1
)

Notes:

  • This function reuses outputs from the initial catcheR_10Xcatch run.

  • Arguments and outputs are otherwise the same as catcheR_10Xcatch().