calculate_sample_corr_distr {proBatch} | R Documentation

## Calculates correlation for all pairs of the samples in data matrix, labels as replicated/same_batch/unrelated in output columns (see "Value").

### Description

Calculates correlation for all pairs of the samples in data matrix, labels as replicated/same_batch/unrelated in output columns (see "Value").

### Usage

    calculate_sample_corr_distr(
      data_matrix,
      sample_annotation,
      repeated_samples = NULL,
      biospecimen_id_col = "EarTag",
      sample_id_col = "FullRunName",
      batch_col = "MS_batch"
    )

### Arguments

`data_matrix` | features (in rows) vs samples (in columns) matrix, with feature IDs in rownames and file/sample names as colnames. See "example_proteome_matrix" for more details (to call the description, use `help("example_proteome_matrix")`)
`sample_annotation` | data frame with: `sample_id_col` (this can be repeated as row names) biological covariates technical covariates (batches etc) . See `help("example_sample_annotation")`
`repeated_samples` | vector of sample IDs to evaluate, if `NULL`, all samples are taken into account for plotting
`biospecimen_id_col` | column in `sample_annotation` that defines a unique bio ID, which is usually a combination of conditions or groups. Tip: if such ID is absent, but can be defined from several columns, create new `biospecimen_id` column
`sample_id_col` | name of the column in `sample_annotation` table, where the filenames (colnames of the `data_matrix` are found).
`batch_col` | column in `sample_annotation` that should be used for batch comparison (or other, non-batch factor to be mapped to color in plots).

### Value

dataframe with the following columns, that are suggested to use for plotting in `plot_sample_corr_distribution` as `plot_param`:

1. `replicate`

2. `batch_the_same`

3. `batch_replicate`

4. `batches`

other columns are:

1. `sample_id_1` & `sample_id_2`, both generated from `sample_id_col` variable

2. `correlation` - correlation of two corresponding samples

3. `batch_1` & `batch_2` or analogous, created the same as `sample_id_1`

### Examples

    corr_distribution = calculate_sample_corr_distr(data_matrix = example_proteome_matrix,
    sample_annotation = example_sample_annotation,
    batch_col = 'MS_batch',biospecimen_id_col = "EarTag")

[Package proBatch version 1.11.0 Index]