calculate_sample_corr_distr: Calculates correlation for all pairs of the samples in data...

In proBatch: Tools for Diagnostics and Corrections of Batch Effects in Proteomics

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")

proBatch documentation built on Nov. 8, 2020, 4:55 p.m.