aggregate_duplicates-methods: Aggregates multiple counts from the same samples (e.g., from...

In stemangiola/ttBulk: Brings transcriptomics to the tidyverse

Aggregates multiple counts from the same samples (e.g., from isoforms), concatenates other character columns, and averages other numeric columns

Description

aggregate_duplicates() takes as input A 'tbl' (with at least three columns for sample, feature and transcript abundance) or 'SummarizedExperiment' (more convenient if abstracted to tibble with library(tidySummarizedExperiment)) and returns a consistent object (to the input) with aggregated transcripts that were duplicated.

Usage

aggregate_duplicates(
  .data,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL,
  aggregation_function = sum,
  keep_integer = TRUE
)

## S4 method for signature 'spec_tbl_df'
aggregate_duplicates(
  .data,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL,
  aggregation_function = sum,
  keep_integer = TRUE
)

## S4 method for signature 'tbl_df'
aggregate_duplicates(
  .data,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL,
  aggregation_function = sum,
  keep_integer = TRUE
)

## S4 method for signature 'tidybulk'
aggregate_duplicates(
  .data,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL,
  aggregation_function = sum,
  keep_integer = TRUE
)

## S4 method for signature 'SummarizedExperiment'
aggregate_duplicates(
  .data,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL,
  aggregation_function = sum,
  keep_integer = TRUE
)

## S4 method for signature 'RangedSummarizedExperiment'
aggregate_duplicates(
  .data,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL,
  aggregation_function = sum,
  keep_integer = TRUE
)

Arguments

.data	A 'tbl' (with at least three columns for sample, feature and transcript abundance) or 'SummarizedExperiment' (more convenient if abstracted to tibble with library(tidySummarizedExperiment))
.sample	The name of the sample column
.transcript	The name of the transcript/gene column
.abundance	The name of the transcript/gene abundance column
aggregation_function	A function for counts aggregation (e.g., sum, median, or mean)
keep_integer	A boolean. Whether to force the aggregated counts to integer

Details

'r lifecycle::badge("maturing")'

This function aggregates duplicated transcripts (e.g., isoforms, ensembl). For example, we often have to convert ensembl symbols to gene/transcript symbol, but in doing so we have to deal with duplicates. 'aggregate_duplicates' takes a tibble and column names (as symbols; for 'sample', 'transcript' and 'count') as arguments and returns a tibble with aggregate transcript with the same name. All the rest of the column are appended, and factors and boolean are appended as characters.

Underlying custom method: data |> filter(n_aggr > 1) |> group_by(!!.sample,!!.transcript) |> dplyr::mutate(!!.abundance := !!.abundance |> aggregation_function())

Value

A consistent object (to the input) with aggregated transcript abundance and annotation

A consistent object (to the input) with aggregated transcript abundance and annotation

A consistent object (to the input) with aggregated transcript abundance and annotation

A consistent object (to the input) with aggregated transcript abundance and annotation

A 'SummarizedExperiment' object

A 'SummarizedExperiment' object

Examples

# Create a aggregation column
se_mini = tidybulk::se_mini
SummarizedExperiment::rowData(se_mini )$gene_name = rownames(se_mini )

   aggregate_duplicates(
     se_mini,
   .transcript = gene_name
   )

stemangiola/ttBulk documentation built on Dec. 14, 2024, 6:12 a.m.