mkAssay {TBSignatureProfiler} | R Documentation |
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 |
input_name |
a character string specifying the name of the assay to
be referenced for creating additional assays. Default is |
output_name |
a character string to concatenate to "log" when computing
a log assay. If |
log |
logical. Indicate whether an assay returned should be the log
of whichever assay is specified in |
counts_to_CPM |
logical. This argument only applies if the
|
prior_counts |
an integer specifying the average count to be added to
each observation to avoid taking the log of zero. Used only if
|
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.
|
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