threshold_SE: Threshold SE

In dunbarlabNIH/barcodetrackR: Functions for Analyzing Cellular Barcoding Data

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
)

dunbarlabNIH/barcodetrackR documentation built on April 26, 2021, 6:20 p.m.