QC_generator

QC_generator

QC_generator

Public fields

lfqdata

lfqdata

lfqdata_prot

lfqdata_prot

lfqdata_prot_IBAQ

lfqdata_prot_IBAQ

lfqdata_prot_transformed

lfqdata_prot_transformed (VSN normalized)

protein_annotation

protein_annotation

lfqdata_peptide

lfqdata_peptide

lfqdata_peptide_transformed

lfqdata_peptide_transformed (VSN normalized)

output_dir

output_dir

GRP2

GRP2

TABLES2WRITE

TABLES2WRITE

links

links

Methods

Public methods

• QC_generator$new()

• QC_generator$get_peptides_wide()

• QC_generator$get_peptides_transformed()

• QC_generator$get_peptides_transformed_wide()

• QC_generator$get_annotation()

• QC_generator$get_prot_data()

• QC_generator$get_prot_wide()

• QC_generator$get_prot_transformed()

• QC_generator$get_prot_transformed_wide()

• QC_generator$get_prot_IBAQ()

• QC_generator$get_protein_per_group_abundance()

• QC_generator$get_protein_per_group_abundance_with_row_annot()

• QC_generator$get_protein_per_group_abundance_wide()

• QC_generator$get_prot_IBAQ_wide()

• QC_generator$get_list()

• QC_generator$write_xlsx()

• QC_generator$copy_dataset()

• QC_generator$render_QC_protein_abundances()

• QC_generator$render_sample_size_QC()

• QC_generator$render_index_html()

• QC_generator$render_index_md()

• QC_generator$get_protein_per_group_small_wide()

• QC_generator$clone()

---

Method new()

initialize

Usage

QC_generator$new(lfqdata, protein_annotation, prolfquapp_config)

Arguments

lfqdata

LFQData object

protein_annotation

ProteinAnnotation object

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.