Function to convert to WSPmm format — create.count.data.WSPmm • wispack

This function converts a data frame of MERFISH data produced by the cortical_coordinate_transform function into a count data format suitable for input into the WSPmm model. The function bins the data along a specified dimension (either x or y), collapses along the other dimension, and includes specified genes and fixed effects in the output. The resulting count data frame contains counts for each gene in each cell, along with associated metadata such as bin number, context, mouse identifier, and cell number.

Usage

create.count.data.WSPmm(
  df.merfish,
  bin.dim = c("x_bins", "y_bins"),
  gene.list,
  fixed.effect.names,
  context = NULL
)

Arguments

df.merfish: A data frame of MERFISH data produced by the cortical_coordinate_transform function
bin.dim: A character string specifying the dimension by which to bin the data; must be either "x_bins" or "y_bins"
gene.list: A character vector of genes to include in the count data, which will form the "species" level of the model
fixed.effect.names: A character vector of column names in df.merfish to include as fixed effects in the count data
context: A character string specifying the context level for fixed effects; if NULL, will use "context"

Value

A data frame in count data format suitable for input into the WSPmm model