threshold_SE {barcodetrackR} | R Documentation

## Threshold SE

### Description

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.

### Usage

    threshold_SE(
      your_SE,
      threshold_value,
      threshold_type = "relative",
      verbose = TRUE
    )

### Arguments

`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.

### Value

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.

### Examples

    data(wu_subset)
    threshold_SE(
        your_SE = wu_subset, threshold_value = 0.005,
        threshold_type = "relative", verbose = TRUE
    )

[Package barcodetrackR version 1.2.0 Index]