define_sample_order: Defining sample order internally

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

Defining sample order internally

Description

Defining sample order internally

Usage

define_sample_order(order_col, sample_annotation, facet_col, batch_col,
  df_long, sample_id_col, color_by_batch)

Arguments

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
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")
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'
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).
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.
sample_id_col	name of the column in sample_annotation table, where the filenames (colnames of the data_matrix are found).
color_by_batch	(logical) whether to color points and connecting lines by batch factor as defined by batch_col.

Value

list of two items: order_col new name and new df_long

See Also

plot_sample_mean_or_boxplot, feature_level_diagnostics

Examples

sample_order = define_sample_order(order_col = 'order', 
sample_annotation = example_sample_annotation, 
facet_col = NULL, batch_col = 'MS_batch', df_long = example_proteome, 
sample_id_col = 'FullRunName', color_by_batch = TRUE)
new_order_col = sample_order$order_col
df_long = sample_order$df_long

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