QC_generator
Description
QC_generator
QC_generator
Public fields
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lfqdata - lfqdata
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lfqdata_prot - lfqdata_prot
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lfqdata_prot_IBAQ - lfqdata_prot_IBAQ
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lfqdata_prot_transformed - lfqdata_prot_transformed (VSN normalized)
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protein_annotation - protein_annotation
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lfqdata_peptide - lfqdata_peptide
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lfqdata_peptide_transformed - lfqdata_peptide_transformed (VSN normalized)
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output_dir - output_dir
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GRP2 - GRP2
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TABLES2WRITE - TABLES2WRITE
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links - links
Methods
Public methods
Method new()
initialize
Usage
QC_generator\$new(lfqdata, protein_annotation, prolfquapp_config)
Arguments
-
lfqdata - LFQData object
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protein_annotation - ProteinAnnotation object
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prolfquapp_config - ProlfquAppConfig object
Method get_peptides_wide()
get peptides in wide format
Usage
QC_generator\$get_peptides_wide()
Returns
peptide data in wide format
Method get_peptides_transformed()
get VSN-transformed peptide data
Usage
QC_generator\$get_peptides_transformed()
Returns
VSN-transformed peptide LFQData
Method get_peptides_transformed_wide()
get VSN-transformed peptide data in wide format
Usage
QC_generator\$get_peptides_transformed_wide()
Returns
VSN-transformed peptide data in wide format
Method get_annotation()
get annotation data
Usage
QC_generator\$get_annotation()
Returns
annotation data.frame
Method get_prot_data()
get protein data
Usage
QC_generator\$get_prot_data()
Returns
protein LFQData
Method get_prot_wide()
get protein data in wide format
Usage
QC_generator\$get_prot_wide()
Returns
protein data in wide format
Method get_prot_transformed()
get VSN-transformed protein data
Usage
QC_generator\$get_prot_transformed()
Returns
VSN-transformed protein LFQData
Method get_prot_transformed_wide()
get VSN-transformed protein data in wide format
Usage
QC_generator\$get_prot_transformed_wide()
Returns
VSN-transformed protein data in wide format
Method get_prot_IBAQ()
get IBAQ protein data
Usage
QC_generator\$get_prot_IBAQ()
Returns
IBAQ protein LFQData
Method get_protein_per_group_abundance()
get protein abundance per group
Usage
QC_generator\$get_protein_per_group_abundance()
Returns
protein abundance per group
Method get_protein_per_group_abundance_with_row_annot()
get protein abundance per group with row annotation
Usage
QC_generator\$get_protein_per_group_abundance_with_row_annot()
Returns
protein abundance per group with annotation
Method get_protein_per_group_abundance_wide()
get protein abundance per group in wide format
Usage
QC_generator\$get_protein_per_group_abundance_wide()
Returns
protein abundance per group in wide format
Method get_prot_IBAQ_wide()
get IBAQ protein data in wide format
Usage
QC_generator\$get_prot_IBAQ_wide()
Returns
IBAQ protein data in wide format
Method get_list()
get list of all tables
Usage
QC_generator\$get_list()
Returns
list of tables
Method write_xlsx()
write tables to xlsx file
Usage
QC_generator\$write_xlsx()
Method copy_dataset()
copy dataset/annotation file to output directory
Usage
QC_generator\$copy_dataset(dataset_path)
Arguments
-
dataset_path - path to the dataset file
Method render_QC_protein_abundances()
render QC protein abundances report
Usage
QC_generator\$render_QC_protein_abundances()
Method render_sample_size_QC()
render sample size QC report
Usage
QC_generator\$render_sample_size_QC()
Method render_index_html()
render index HTML file
Usage
QC_generator\$render_index_html()
Method render_index_md()
render index markdown file
Usage
QC_generator\$render_index_md()
Method get_protein_per_group_small_wide()
get protein per group small wide format
Usage
QC_generator\$get_protein_per_group_small_wide()
Returns
protein per group data in small wide format
Method clone()
The objects of this class are cloneable with this method.
Usage
QC_generator\$clone(deep = FALSE)
Arguments
-
deep - Whether to make a deep clone.