check_sample_consistency: Check if sample annotation is consistent with data matrix and...

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

Check if sample annotation is consistent with data matrix and join the two

Description

Check if sample annotation is consistent with data matrix and join the two

Usage

check_sample_consistency(sample_annotation, sample_id_col, df_long,
  batch_col = NULL, order_col = NULL, facet_col = NULL,
  merge = TRUE)

Arguments

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")
sample_id_col	name of the column in sample_annotation table, where the filenames (colnames of the data_matrix are found).
df_long	data frame where each row is a single feature in a single sample. It minimally has a sample_id_col, a feature_id_col and a measure_col, but usually also an m_score (in OpenSWATH output result file). See help("example_proteome") for more details.
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).
order_col	column in sample_annotation that determines sample order. It is used for in initial assessment plots (plot_sample_mean_or_boxplot) and feature-level diagnostics (feature_level_diagnostics). Can be 'NULL' if sample order is irrelevant (e.g. in genomic experiments). For more details, order definition/inference, see define_sample_order and date_to_sample_order
facet_col	column in sample_annotation with a batch factor to separate plots into facets; usually 2nd to batch_col. Most meaningful for multi-instrument MS experiments (where each instrument has its own order-associated effects (see order_col) or simultaneous examination of two batch factors (e.g. preparation day and measurement day). For single-instrument case should be set to 'NULL'
merge	(logical) whether to merge df_long with sample_annotation or not

Value

df_long format data frame, merged with sample_annotation using inner_join (samples represented in both)

Examples

df_test = check_sample_consistency(sample_annotation = example_sample_annotation, 
df_long = example_proteome, sample_id_col = 'FullRunName',
batch_col = NULL, order_col = NULL, facet_col = NULL)

symbioticMe/proBatch documentation built on April 9, 2023, 11:59 a.m.