FindMarkers: FindMarkers

In tangchao7498/ICAS:

Description

SJ expression markers of identity classes

Arguments

object	ICASDataSet object
ident.1	Identity class to define markers for
ident.2	A second identity class for comparison. If NULL (default) - use all other cells for comparison.
genes.use	SJs to test. Default is to use all SJs
delta.threshold	Limit testing to SJs which show, on average, at least delta.threshold between the two groups of samples. Default is 0.1 Increasing delta.threshold speeds up the function, but can miss weaker signals.
test.use	Denotes which test to use. Available options are: "wilcox" : Wilcoxon rank sum test "bimod" : Likelihood-ratio test for SJ expression, (McDavid et al., Bioinformatics, 2013) "roc" : Standard AUC classifier "t" : Student's t-test "WD" : waldtest for binomial glm "tobit" : Tobit-test for differential SJ expression (Trapnell et al., Nature Biotech, 2014) (default) "poisson" : Likelihood ratio test assuming an underlying poisson distribution. Use only for UMI-based datasets "negbinom" : Likelihood ratio test assuming an underlying negative binomial distribution. Use only for UMI-based datasets "MAST" : GLM-framework that treates cellular detection rate as a covariate (Finak et al, Genome Biology, 2015) "Hyper" : DE based on Hypergeometric test "BB" : DE based on a generalized linear models using betabinomial distribution
min.pct	only test SJs that are detected in a minimum fraction of min.pct cells in either of the two populations. Meant to speed up the function by not testing SJs that are very infrequently expressed. Default is 0.1
min.diff.pct	only test SJs that show a minimum difference in the fraction of detection between the two groups. Set to -Inf by default
only.pos	Only return positive markers (FALSE by default)
print.bar	Print a progress bar once expression testing begins (uses pbapply to do this)
max.cells.per.ident	Down sample each identity class to a max number. Default is no downsampling. Not activated by default (set to Inf)
random.seed	Random seed for downsampling
min.cells.gene	Minimum number of cells expressing the SJ in at least one of the two groups, currently only used for poisson and negative binomial tests
maxit	(Only for test.use is BB) maximum number of (usually Fisher-scoring) iterations allowed. Decreasing maxit speeds up the function, but can weaken statistical reliability.
confounder	(Only for test.use is BB) The confounder to regress out.
min.cells.group	Minimum number of cells in one of the groups
NT	cores for parallel (Currently only support roc test)
...	Additional parameters to pass to specific DE functions

Details

Finds markers (differentially expressed SJs) for identity classes

p-value adjustment is performed using bonferroni correction based on the total number of SJs in the dataset. Other correction methods are not recommended, as ICAS pre-filters SJs using the arguments above, reducing the number of tests performed. Lastly, as Aaron Lun has pointed out, p-values should be interpreted cautiously, as the SJs used for clustering are the same SJs tested for differential expression.

Value

Matrix containing a ranked list of putative markers, and associated statistics (p-values, ROC score, etc.)

References

Seurat

See Also

MASTDETest, and DESeq2DETest for more information on these methods

NegBinomDETest

Seurat

tangchao7498/ICAS documentation built on Jan. 28, 2021, 3:56 p.m.