threshold_SE {barcodetrackR} | R Documentation |
Removes barcodes from a SummarizedExperiment object which have an abundance lower than the provided relative or absolute threshold. See the function 'estimate_barcode_threshold' to estimate an appropriate threshold for an SE.
threshold_SE( your_SE, threshold_value, threshold_type = "relative", verbose = TRUE )
your_SE |
A Summarized Experiment object. |
threshold_value |
Numeric. The minimum threshold abundance for a barcode to be maintained in the SE. If 'threshold_type' is relative, this parameter should be between 0 and 1. If 'threshold_type' is absolute, this parameter should be greater than 1. |
threshold_type |
Character. One of "relative" or "absolute" relative. If a relative threshold is specified, only those rows which have higher than 'threshold_value' proportion of reads within at least one sample will be kept as non-zero. If an absolute threshold is specified, only those rows which have an absolute read count higher than 'threshold_value' in at least one sample will be kept as non-zero. |
verbose |
Logical. If TRUE, print the total number of barcodes removed from the SE. |
Returns a SummarizedExperiment containing only barcodes which passed the supplied threshold in at least one sample. All of the defualt assays are re-calculated after thresholding is applied. Note that since tthe SE is re-instantiated, any custom assays should be recalculated after thresholding.
data(wu_subset) threshold_SE( your_SE = wu_subset, threshold_value = 0.005, threshold_type = "relative", verbose = TRUE )