aggregate_duplicates {tidybulk} | R Documentation

## 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' formatted as | <SAMPLE> | <TRANSCRIPT> | <COUNT> | <...> | and returns a 'tbl' 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' formatted as | <SAMPLE> | <TRANSCRIPT> | <COUNT> | <...> |
`.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

### Value

A 'tbl' object with aggregated transcript abundance and annotation

A 'tbl' object with aggregated transcript abundance and annotation

A 'tbl' object with aggregated transcript abundance and annotation

A 'tbl' object with aggregated transcript abundance and annotation

A 'SummarizedExperiment' object

A 'SummarizedExperiment' object

### Examples

        aggregate_duplicates(
        tidybulk::se_mini,
        aggregation_function = sum
        )

[Package tidybulk version 1.4.0 Index]