check_sample_consistency {proBatch} | R Documentation |
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)
[Package
proBatch version 1.9.0
Index]