define_sample_order {proBatch} | R Documentation |
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
[Package
proBatch version 1.10.0
Index]