metamorphr (version 0.2.0)

collapse_mean: Collapse intensities of technical replicates by calculating their mean

Description

Calculates the mean of the intensity of technical replicates (e.g., if the same sample was injected multiple times or if multiple workups have been performed on the same starting material). The function assigns new sample names by joining either group and replicate name, or if a batch column is specified group, replicate and batch together with a specified separator. Due to the nature of the function, sample and feature metadata columns will be dropped unless they are specified with the according arguments.

Usage

collapse_mean(
  data,
  group_column = .data$Group,
  replicate_column = .data$Replicate,
  batch_column = .data$Batch,
  feature_metadata_cols = "Feature",
  sample_metadata_cols = NULL,
  separator = "_"
)

Value

A tibble with intensities of technical replicates collapsed.

Arguments

data

A tidy tibble created by read_featuretable.

group_column

Which column should be used for grouping? Usually grouping_column = Group. Uses args_data_masking.

replicate_column

Which column contains replicate information? Usually replicate_column = Replicate. Uses args_data_masking.

batch_column

Which column contains batch information? If all samples belong to the same batch (i.e., they all have the same batch identifier in the batch_column) it will have no effect on the calculation. Usually batch_column = Batch. Uses args_data_masking.

feature_metadata_cols

A character or character vector containing the names of the feature metadata columns. They are usually created when reading the feature table with read_featuretable. Feature metadata columns not specified here will be dropped.

sample_metadata_cols

A character or character vector containing the names of the sample metadata columns. They are usually created when joining the metadata with join_metadata. Sample metadata columns not specified here will be dropped, except for group_column, replicate_column and batch_column if specified.

separator

Separator used for joining group and replicate, or group, batch and replicate together to create the new sample names. The new sample names will be Group name, separator, Batch name, separator, Replicate name, or Group name, separator, Replicate name, in case all samples belong to the same batch (i.e., they all have the same batch identifier in the batch_column).

Examples

# uses a slightly modified version of toy_metaboscape_metadata
collapse_toy_metaboscape_metadata <- toy_metaboscape_metadata
collapse_toy_metaboscape_metadata$Replicate <- 1

toy_metaboscape %>%
  join_metadata(collapse_toy_metaboscape_metadata) %>%
  impute_lod() %>%
  collapse_mean(group_column = Group, replicate_column = Replicate)