get_limma_top_table_with_ci: get_limma_top_table_with_ci

In MonashBioinformaticsPlatform/celaref: Single-cell RNAseq cell cluster labelling by reference

Description

Internal function that wraps limma topTable output but also adds upper and lower confidence intervals to the logFC. Calculated according to https://support.bioconductor.org/p/36108/

Usage

get_limma_top_table_with_ci(fit2, the_coef, ci = 0.95)

Arguments

fit2	The fit2 object after calling eBayes as per standard limma workflow. Ie object that topTable gets called on.
the_coef	Coeffient. As passed to topTable.
ci	Confidence interval. Number between 0 and 1, default 0.95 (95%)

Value

Output of topTable, but with the (95 for the logFC.

See Also

contrast_the_group_to_the_rest_with_limma_for_microarray Calling function.

MonashBioinformaticsPlatform/celaref documentation built on June 5, 2019, 11:35 a.m.