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b/man/getDiffExp.Rd |
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% Generated by roxygen2: do not edit by hand |
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% Please edit documentation in R/differentialexpression.R |
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\name{getDiffExp} |
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\alias{getDiffExp} |
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\title{getDiffExp} |
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\usage{ |
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getDiffExp( |
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object, |
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assay = NULL, |
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group.by, |
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group.base = NULL, |
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covariates = NULL, |
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method = "DESeq2" |
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) |
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} |
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\arguments{ |
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\item{object}{a VoltRon object} |
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\item{assay}{assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see \link{SampleMetadata}. |
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if NULL, the default assay will be used, see \link{vrMainAssay}.} |
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\item{group.by}{the categorical variable from metadata to get differentially expressed features across} |
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\item{group.base}{Optional, the base category in \code{group.by} which is used as control group} |
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\item{covariates}{the covariate variable for the design formula} |
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\item{method}{the method for DE analysis, e.g. DESeq2} |
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} |
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\description{ |
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Get differential expression with DESeq2 |
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} |