limmaDS | R Documentation |
Performs differential expression analysis using LIMMA
limmaDS(
Set,
variable_names,
covariable_names,
type,
contrasts,
levels,
coef,
sva,
annotCols,
method,
robust,
normalization,
voomQualityWeights,
big,
sort.by
)
Set |
either a |
variable_names |
grouping variable used to perform differential expression analysis |
covariable_names |
name of variables used in the adjusted models |
type |
... |
contrasts |
... |
levels |
... |
coef |
... |
sva |
should differential expression analysis be adjusted by SVA? |
annotCols |
variables from the annotation data used in the output |
method |
String indicating the method used in the regression (e.g. lmFit function of limma: "ls" or "robust". (Default: "ls") |
robust |
Logical value indicating whether robust method is applied in the eBayes function of limma. Default is FALSE. |
normalization |
String indicating the normalize method used when using voom for RNAseq data (see normalized.method argument in limma::vomm) |
voomQualityWeights |
Logical value indicating whether limma::voomWithQualityWeights should be used instead of limma::voom. |
big |
Logical value indicating whether SmartSVA should be used instead of SVA (TRUE recommended for methylation or when having large number of samples). |
a matrix with genes ordered by p-value
Gonzalez, JR.
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