runSoupX | R Documentation |
A wrapper function for autoEstCont and adjustCounts. Identify potential contamination from experimental factors such as ambient RNA. Visit their vignette for better understanding.
runSoupX(
inSCE,
sample = NULL,
useAssay = "counts",
background = NULL,
bgAssayName = NULL,
bgBatch = NULL,
assayName = ifelse(is.null(background), "SoupX", "SoupX_bg"),
cluster = NULL,
reducedDimName = ifelse(is.null(background), "SoupX_UMAP_", "SoupX_bg_UMAP_"),
tfidfMin = 1,
soupQuantile = 0.9,
maxMarkers = 100,
contaminationRange = c(0.01, 0.8),
rhoMaxFDR = 0.2,
priorRho = 0.05,
priorRhoStdDev = 0.1,
forceAccept = FALSE,
adjustMethod = c("subtraction", "soupOnly", "multinomial"),
roundToInt = FALSE,
tol = 0.001,
pCut = 0.01
)
inSCE |
A SingleCellExperiment object. |
sample |
A single character specifying a name that can be found in
|
useAssay |
A single character string specifying which assay in
|
background |
A numeric matrix of counts or a
SingleCellExperiment object with the matrix in |
bgAssayName |
A single character string specifying which assay in
|
bgBatch |
The same thing as |
assayName |
A single character string of the output corrected matrix.
Default |
cluster |
Prior knowledge of clustering labels on cells. A single
character string for specifying clustering label stored in
|
reducedDimName |
A single character string of the prefix of output
corrected embedding matrix for each sample. Default |
tfidfMin |
Numeric. Minimum value of tfidf to accept for a marker gene.
Default |
soupQuantile |
Numeric. Only use genes that are at or above this
expression quantile in the soup. This prevents inaccurate estimates due to
using genes with poorly constrained contribution to the background. Default
|
maxMarkers |
Integer. If we have heaps of good markers, keep only the
best maxMarkers of them. Default |
contaminationRange |
Numeric vector of two elements. This constrains
the contamination fraction to lie within this range. Must be between 0 and 1.
The high end of this range is passed to
|
rhoMaxFDR |
Numeric. False discovery rate passed to
|
priorRho |
Numeric. Mode of gamma distribution prior on contamination
fraction. Default |
priorRhoStdDev |
Numeric. Standard deviation of gamma distribution prior
on contamination fraction. Default |
forceAccept |
Logical. Should we allow very high contamination fractions
to be used. Passed to |
adjustMethod |
Character. Method to use for correction. One of
|
roundToInt |
Logical. Should the resulting matrix be rounded to
integers? Default |
tol |
Numeric. Allowed deviation from expected number of soup counts.
Don't change this. Default |
pCut |
Numeric. The p-value cut-off used when
|
The input inSCE
object with soupX_nUMIs
,
soupX_clustrers
, soupX_contamination
appended to colData
slot; soupX_{sample}_est
and soupX_{sample}_counts
for each
sample appended to rowData
slot; and other computational metrics at
getSoupX(inSCE)
. Replace "soupX" to "soupX_bg" when background
is used.
Yichen Wang
plotSoupXResults
## Not run:
# SoupX does not work for toy example,
sce <- importExampleData("pbmc3k")
sce <- runSoupX(sce, sample = "sample")
plotSoupXResults(sce, sample = "sample")
## End(Not run)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.