melt_gct: Transform a GCT object in to a long form 'data.table' (aka...

In cmapR: CMap Tools in R

Description

Utilizes the melt.data.table function to transform the matrix into long form. Optionally can include the row and column annotations in the transformed data.table.

Usage

melt.gct(...)

melt_gct(
  g,
  suffixes = NULL,
  remove_symmetries = FALSE,
  keep_rdesc = TRUE,
  keep_cdesc = TRUE,
  ...
)

## S4 method for signature 'GCT'
melt_gct(
  g,
  suffixes = NULL,
  remove_symmetries = FALSE,
  keep_rdesc = TRUE,
  keep_cdesc = TRUE,
  ...
)

Arguments

...	further arguments passed along to data.table::merge
g	the GCT object
suffixes	the character suffixes to be applied if there are collisions between the names of the row and column descriptors
remove_symmetries	boolean indicating whether to remove the lower triangle of the matrix (only applies if g@mat is symmetric)
keep_rdesc	boolean indicating whether to keep the row descriptors in the final result
keep_cdesc	boolean indicating whether to keep the column descriptors in the final result

Value

a data.table object with the row and column ids and the matrix values and (optinally) the row and column descriptors

See Also

Other GCT utilities: annotate.gct(), merge.gct(), rank.gct(), subset.gct()

Examples

# simple melt, keeping both row and column meta
head(melt_gct(ds))

# update row/colum suffixes to indicate rows are genes, columns experiments
head(melt_gct(ds, suffixes = c("_gene", "_experiment")))

# ignore row/column meta
head(melt_gct(ds, keep_rdesc = FALSE, keep_cdesc = FALSE))

cmapR documentation built on Dec. 12, 2020, 2 a.m.