Description Usage Arguments Value
View source: R/uSort_preProcess.R
An outlier detection function identifies cells with median expression below that of the bulk, reproduced from FluidigmSC package.
1 2 3 4 | 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)
|
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. |
A vector of character stating the IDs of outlier cells.
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