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

Description Usage Arguments Value Author(s) Examples

Given an input of a Summarized Experiment with a counts or CPM assay, This function creates additional assays for a gene expression count dataset to be used in further analysis.

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

`SE_obj`	a `SummarizedExperiment` object containing gene expression 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 concatenate to "log" when computing a log assay. If `NULL`, then `input_name` will be substituted. Only used if `log = TRUE`. Default is `NULL`.
`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`	an 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`.

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

`cpm`	Counts per million
`logcpm`	Log counts per million
`log_<output_name>`	Log of original inputted assay. `<output_name>` will be replaced by inputted parameter.

Aubrey Odom

# 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