fx_calcESvsRest | R Documentation |
Internal function. See CalcDEvsRest
.
fx_calcESvsRest(nge, cl, CGS, exponent, pseudocount, DRthresh)
nge |
The log-normalized gene expression matrix. |
cl |
The factor with cluster assignments per cell (column of nge). |
CGS |
The output from |
exponent |
A length-one numeric vector representing the
base of the log-normalized gene expression data to be processed. Generally
gene expression data is transformed into log2 space when normalizing (set
this to 2), though |
pseudocount |
A length-one numeric vector representing the pseudocount added to all log-normalized values in your input data. Most methods use a pseudocount of 1 to eliminate log(0) errors. If you are using data that has not been log-transformed (for example, corrected counts from SCTransform), set this to NA. |
DRthresh |
The threshold for minimum detection rate of a gene in the cluster for the gene to be considered in the following Wilcoxon rank-sum test. |
Calculates the log-ratios of gene expression for all genes in each one-vs-all comparison of a cluster vs the rest of the data. This is used to determine the genes used in DEvsRest calculations.
The function returns a list where each list element is the log-ratios
of gene expression when comparing each gene in a cluster to the rest of the
cells as a whole in a one vs all comparison. These logGER tables are
filtered to only include those gene that pass logGER threshold, and thus
the names for each list entry correspond to the genes to test in
fx_calcDEvsRest
.
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