get_sample_corr_distrib {proBatch}R Documentation

Calculates correlation distribution for all pairs of the replicated samples

Description

Calculates correlation distribution for all pairs of the replicated samples

Usage

get_sample_corr_distrib(cor_proteome, sample_annotation,
  sample_id_col = "FullRunName", biospecimen_id_col = "EarTag",
  batch_col = "batch")

Arguments

cor_proteome

sample correlation matrix (square)

sample_annotation

data matrix with:

  1. sample_id_col (this can be repeated as row names)

  2. biological covariates

  3. technical covariates (batches etc)

sample_id_col

name of the column in sample_annotation file, where the filenames (colnames of the data matrix are found)

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

batch_col

column in sample_annotation that should be used for batch comparison

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


[Package proBatch version 1.0.0 Index]