fluidigmSC_identifyExpOutliers: An outlier detection function

Description Usage Arguments Value

View source: R/uSort_preProcess.R

Description

An outlier detection function identifies cells with median expression below that of the bulk, reproduced from FluidigmSC package.

Usage

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fluidigmSC_identifyExpOutliers(log2ex_data, expression_data_raw, threshold,
  step, fine_step, num_fine_test, pct_goodsample_threshold = 0.5,
  quantile_threshold = 0.95, low_quantile_threshold = 0.25,
  min_gene_number = 25, lod)

Arguments

log2ex_data

A data frame containing log2 tranformed expression values, with rownames of genes and colnames of cells.

expression_data_raw

A data frame containing raw expression values, with rownames of genes and colnames of cells.

threshold

A value in raw expression used as the starting threshold value.

step

An integer number indicating the increment of threshold value at each iteration.

fine_step

An integer number indicating the increment of threshold value at each iteration, at the refining stage.

num_fine_test

An integer number indicating the number of iteration of the refining stage.

pct_goodsample_threshold

A fraction value indicating the minimum percentage of samples on which the representative genes are detectable.

quantile_threshold

A probability of gene detection rate above which a sample is considered as good sample.

low_quantile_threshold

A probability of average gene expression value below which a sample is taken as an outlier.

min_gene_number

An integer indicating the minimum size of representative genes.

lod

A value of limit of detection in the unit of TPM/CPM/RPKM.

Value

A vector of character stating the IDs of outlier cells.


uSORT documentation built on May 2, 2018, 4:04 a.m.