comparison_standardizeHeights: Standardize height values of a scan by centering/scaling by...

In cmcR: An Implementation of the 'Congruent Matching Cells' Method

Standardize height values of a scan by centering/scaling by desired statistics and replacing missing values

Description

Standardize height values of a scan by centering/scaling by desired statistics and replacing missing values

Usage

comparison_standardizeHeights(
  heightValues,
  withRespectTo = "individualCell",
  centerBy = mean,
  scaleBy = sd
)

Arguments

heightValues	list/tibble column of x3p objects
withRespectTo	currently ignored
centerBy	statistic by which to center (i.e., subtract from) the height values
scaleBy	statistic by which to scale (i.e., divide) the height values

Value

A list of the same length as the input containing x3p objects with standardized surface matrices

Note

this function adds information to the metainformation of the x3p scan it is given that is required for calculating, for example, the pairwise-complete correlation using the comparison_cor function.

Examples

data(fadul1.1_processed,fadul1.2_processed)

cellTibble <- fadul1.1_processed %>%
comparison_cellDivision(numCells = c(8,8)) %>%
dplyr::mutate(regionHeightValues = comparison_getTargetRegions(cellHeightValues = cellHeightValues,
                                                               target = fadul1.2_processed)) %>%
dplyr::mutate(cellPropMissing = comparison_calcPropMissing(heightValues = cellHeightValues),
              regionPropMissing = comparison_calcPropMissing(heightValues = regionHeightValues)) %>%
dplyr::filter(cellPropMissing <= .85 & regionPropMissing <= .85) %>%
dplyr::mutate(cellHeightValues = comparison_standardizeHeights(heightValues = cellHeightValues),
             regionHeightValues = comparison_standardizeHeights(heightValues = regionHeightValues))

head(cellTibble)

cmcR documentation built on Dec. 10, 2022, 5:06 p.m.