melt: Melt data from wide to long format
In acidgenomics/r-acidexperiment: Acid Genomics Summarized Experiment

melt	R Documentation

Melt data from wide to long format

Description

Unpivot column data from wide format to long format.

Usage

melt(object, ...)

## S4 method for signature 'Matrix'
melt(
  object,
  colnames = c("rowname", "colname", "value"),
  min = -Inf,
  minMethod = c("absolute", "perRow"),
  trans = c("identity", "log2", "log10")
)

## S4 method for signature 'SummarizedExperiment'
melt(
  object,
  assay = 1L,
  min = -Inf,
  minMethod = c("absolute", "perRow"),
  trans = c("identity", "log2", "log10")
)

Arguments

`object`	Object.
`colnames`	`character(3)`. Column name mappings for melted data frame return.
`min`	`numeric(1)` or `NULL`. Minimum count threshold to apply. Filters using "greater than or equal to" logic internally. Note that this threshold gets applied prior to logarithmic transformation, when `trans` argument applies. Use `-Inf` or `NULL` to disable.
`minMethod`	`character(1)`. Only applies when `min` argument is numeric. Uses `match.arg()`. `absolute`: Applies hard cutoff to `counts` column after the melt operation. This applies to all counts, not per feature. `perRow`: Applies cutoff per row (i.e. gene). Internally, `rowSums()` values are checked against this cutoff threshold prior to the melt operation.
`trans`	`character(1)`. Apply a log transformation (e.g. `log2(x + 1L)`) to the count matrix prior to melting, if desired. Use `"identity"` to return unmodified (default).
`assay`	`vector(1)`. Assay name or index position.
`...`	Additional arguments.

Value

DataFrame.

Note

Updated 2023-10-27.

Examples

data(RangedSummarizedExperiment, package = "AcidTest")

## SummarizedExperiment ====
object <- RangedSummarizedExperiment
dim(object)
x <- melt(object)
nrow(x)
print(x)

acidgenomics/r-acidexperiment documentation built on Jan. 17, 2024, 7:56 p.m.