calcNormCounts {karyotapR} | R Documentation |
Normalize raw counts
Description
Normalizes raw counts from counts
slot in TapestriExperiment
and returns the object with normalized counts in the normcounts
slot.
Also calculates the standard deviation for each probe using normalized counts and adds it to rowData
.
Usage
calcNormCounts(TapestriExperiment, method = "mb", scaling.factor = NULL)
Arguments
TapestriExperiment |
|
method |
Character, normalization method. Default "mb". |
scaling.factor |
Numeric, optional number to scale normalized counts if |
Details
"mb" method performs the same normalization scheme as in Mission Bio's mosaic package for python:
Counts for each barcode are normalized relative to their barcode's mean and probe counts are normalized relative to their probe's median.
"libNorm" method preforms library size normalization, returning the proportion of counts of each probe within a cell.
The proportion is multiplied by scaling.factor
if provided.
Value
TapestriExperiment
object with normalized counts added to normcounts
slot.
Examples
tap.object <- newTapestriExperimentExample() # example TapestriExperiment object
tap.object <- calcNormCounts(tap.object)