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Add midparent expression to SummarizedExperiment object

Source: R/01_data_processing.R
add_midparent_expression.Rd

Add midparent expression to SummarizedExperiment object

Usage

add_midparent_expression(
  se,
  coldata_column = "Generation",
  parent1 = "P1",
  parent2 = "P2",
  method = "mean",
  weights = c(1, 1)
)

Arguments

se

A SummarizedExperiment object with a count matrix and sample metadata.

coldata_column

Character indicating the name of column in colData(se) where information on the generation are stored. Default: "Generation".

parent1

Character indicating which level of the variable coldata_column represents parent 1. Default: "P1".

parent2

Character indicating which level of the variable coldata_column represents parent 2. Default: "P2".

method

Character indicating the method to use to create midparent values. One of 'mean' (default), 'sum', or 'weightedmean'.

weights

Numeric vector of length 2 indicating the weights to give to parents 1 and 2 (respectively) if method == "weightedmean". Setting method == "weightedmean" is used sometimes when parents have different ploidy levels. In such cases, the ploidy levels of parents 1 and 2 can be passed in a vector. Default: c(1, 2).

Value

A SummarizedExperiment object.

Examples

data(se_chlamy)
new_se <- add_midparent_expression(se_chlamy)