resultsTables: Results tables

Description Usage Arguments Details Value Tables Note Examples

Description

Results tables

Usage

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resultsTables(object, ...)

## S4 method for signature 'DESeqResults'
resultsTables(
  object,
  alphaThreshold = NULL,
  lfcThreshold = NULL,
  baseMeanThreshold = NULL,
  return = c("tbl_df", "DataFrameList")
)

## S4 method for signature 'DESeqAnalysis'
resultsTables(object, i, extra = TRUE, ...)

Arguments

object

Object.

alphaThreshold

numeric(1) or NULL. Adjusted P value ("alpha") cutoff. If left NULL, will use the cutoff defined in the object.

lfcThreshold

numeric(1) or NULL. Log (base 2) fold change ratio cutoff threshold. If left NULL, will use the cutoff defined in the object.

baseMeanThreshold

numeric(1) or NULL. Base mean (i.e. average expression across all samples) threshold. If left NULL, will use the cutoff defined in the object. Applies in general to DESeq2 RNA-seq differential expression output.

return

character(1). Type of data frame to return as a list. Uses match.arg().

  • DataFrameList: Returns DataFrameList with row names.

  • tbl_df: Returns list of tbl_df containing "rowname" column.

i

character(1) or integer(1). DESeqResults contrast name or position in results slot.

extra

logical(1). Include row data (i.e. gene metadata) and normalized counts from the internal DESeqDataSet.

...

Additional arguments.

Details

Generate tables summarizing the differential expression, with subsets for differentially expressed genes (DEGs). DEG tables (i.e. everything except the all table), are arranged by adjusted P value.

Value

list. Named list containing subsets of DESeqResults.

Tables

Note

Updated 2020-09-21.

It is generally recommended to not apply post hoc log fold change cutoffs. If a specific effect size is desired, instead run DESeq2::results() using the lfcThreshold parameter. Refer to the DESeq2 documentation and vignette for details.

Examples

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data(deseq)

## DESeqAnalysis ====
x <- resultsTables(deseq, i = 1L)
names(x)

steinbaugh/DESeqAnalysis documentation built on Oct. 15, 2020, 2:02 a.m.