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Add SummarizedExperiment assays to the data structure.

Source: R/bootstrap.R
mkAssay.Rd

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_output_name_cpm

Log counts per million

log_output_name

Log of original input assay.

Author

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
#> class: SummarizedExperiment 
#> dim: 25369 31 
#> metadata(0):
#> assays(2): counts log_counts
#> rownames(25369): DDX11L1 WASH7P ... GOLGA2P3Y GOLGA2P2Y
#> rowData names(0):
#> colnames(31): R01_1 R01_10 ... R02_30 R02_31
#> colData names(2): Sample Disease

# Create a CPM assay
CPM_only <- mkAssay(TB_hiv)
CPM_only
#> class: SummarizedExperiment 
#> dim: 25369 31 
#> metadata(0):
#> assays(2): counts counts_cpm
#> rownames(25369): DDX11L1 WASH7P ... GOLGA2P3Y GOLGA2P2Y
#> rowData names(0):
#> colnames(31): R01_1 R01_10 ... R02_30 R02_31
#> colData names(2): Sample Disease

# Create a logCPM, logcounts, and CPM assay
all_assays <- mkAssay(TB_hiv, log = TRUE)
all_assays
#> class: SummarizedExperiment 
#> dim: 25369 31 
#> metadata(0):
#> assays(4): counts log_counts counts_cpm log_counts_cpm
#> rownames(25369): DDX11L1 WASH7P ... GOLGA2P3Y GOLGA2P2Y
#> rowData names(0):
#> colnames(31): R01_1 R01_10 ... R02_30 R02_31
#> colData names(2): Sample Disease