Skip to contents

Adjust Confounders in a mass_dataset Object

Source: R/method_adjust_confounder.R
adjust_confounder.Rd

This function adjusts for confounders in the expression data of a mass_dataset object. The function takes a list of confounders from the sample_info data and performs a linear regression adjustment on the expression data for each specified confounder.

Usage

adjust_confounder(object, confounder_name_list)

Arguments

object

A mass_dataset object that contains expression data and sample information.

confounder_name_list

A character vector specifying the names of the confounders to adjust for. These names should be columns in the sample_info slot of the mass_dataset object.

Value

A modified mass_dataset object with adjusted expression data where confounders have been accounted for.

Details

This function performs a linear model regression for each feature in the expression data against the specified confounders from the sample information. The residuals of the model are used as the adjusted expression data. If any NA values are present in the confounders or if the confounder names are not found in the sample_info, the function will stop and return an error.

Errors

  • The function will stop if confounder_name_list is empty.

  • The function will stop if any of the confounder names in confounder_name_list are not present in the sample_info.

  • The function will stop if any NA values are present in the specified confounders.

Examples

data("expression_data")
data("sample_info")
data("variable_info")

sample_info$batch <- rep(c(1, 2), length.out = nrow(sample_info))
sample_info$age <- seq_len(nrow(sample_info)) + 20

object <- create_mass_dataset(
  expression_data = expression_data,
  sample_info = sample_info,
  variable_info = variable_info
)

adjusted_object <- adjust_confounder(
  object = object,
  confounder_name_list = c("batch", "age")
)
#> Warning: number of columns of result is not a multiple of vector length (arg 1)

head(extract_expression_data(adjusted_object))
#>               Blank_3 Blank_4 QC_1 QC_2 PS4P1 PS4P2 PS4P3 PS4P4
#> M136T55_2_POS      NA      NA   NA   NA    NA    NA    NA    NA
#> M79T35_POS         NA      NA   NA   NA    NA    NA    NA    NA
#> M307T548_POS       NA      NA   NA   NA    NA    NA    NA    NA
#> M183T224_POS       NA      NA   NA   NA    NA    NA    NA    NA
#> M349T47_POS        NA      NA   NA   NA    NA    NA    NA    NA
#> M182T828_POS       NA      NA   NA   NA    NA    NA    NA    NA