mkAssay: Add SummarizedExperiment assays to the data structure.
In dfjenkins3/TBSignatureProfiler: Profile RNA-Seq Data Using TB Pathway Signatures

mkAssay

R Documentation

Add SummarizedExperiment assays to the data structure.

Description

Given a SummarizedExperiment input with a counts or CPM assay, this function creates additional assays for by computing the CPM, log, or both of the input assay to be used in further analysis.

Usage

mkAssay(
  SE_obj,
  input_name = "counts",
  output_name = NULL,
  log = FALSE,
  counts_to_CPM = TRUE,
  prior_counts = 3
)

Arguments

`SE_obj`	a `SummarizedExperiment` object containing count or CPM data. Required.
`input_name`	a character string specifying the name of the assay to be referenced for creating additional assays. Default is `"counts"`.
`output_name`	a character string to use in place of the `input_name`. If `NULL`, then `input_name` will be substituted. Default is `NULL`. See Return details for how names are altered.
`log`	logical. Indicate whether an assay returned should be the log of whichever assay is specified in `"output_name"`. If `counts_to_CPM = TRUE` as well, then a log CPM assay will also be created. Default is `FALSE`.
`counts_to_CPM`	logical. This argument only applies if the `input_type` is a counts assay. If `TRUE`, then the output assays will include a normalized CPM assay. If `log = TRUE` as well, then a log CPM assay will also be created. Default is `TRUE`.
`prior_counts`	a small integer specifying the average count to be added to each observation to avoid taking the log of zero. Used only if `log = TRUE`. The default is `3`.

Value

This function returns a SummarizedExperiment object with up to 3 additional assay types attached to the original inputted object.

`output_name`_cpm	Counts per million
`log_\code{output_name}_cpm`	Log counts per million
`log_\code{output_name}`	Log of original input assay.

Author(s)

Aubrey Odom-Mabey

Examples

# Create a log assay of the original assay input
# TB_hiv dataset already has counts data
log_only <- mkAssay(TB_hiv, log = TRUE, counts_to_CPM = FALSE)
log_only

# Create a CPM assay
CPM_only <- mkAssay(TB_hiv)
CPM_only

# Create a logCPM, logcounts, and CPM assay
all_assays <- mkAssay(TB_hiv, log = TRUE)
all_assays

dfjenkins3/TBSignatureProfiler documentation built on Oct. 26, 2024, 1:29 a.m.