DEAReportGenerator

Description

DEAReportGenerator

DEAReportGenerator

Details

Generates all output files for a differential expression analysis. Uses a DEAnalyse object as data source instead of the legacy GRP2$RES list.

Public fields

deanalyse

DEAnalyse object containing all analysis results

GRP2

ProlfquAppConfig object containing analysis configuration

fname

filename prefix for DEA results

qcname

filename prefix for QC results

resultdir

directory for storing results

ZIPDIR

zip directory path

Methods

Public methods

• DEAReportGenerator$new()

• DEAReportGenerator$prep_result_list()

• DEAReportGenerator$write_DEA()

• DEAReportGenerator$make_boxplots()

• DEAReportGenerator$filter_data()

• DEAReportGenerator$get_protein_boxplots()

• DEAReportGenerator$contrasts_to_Grob()

• DEAReportGenerator$get_protein_boxplots_contrasts()

• DEAReportGenerator$write_protein_boxplots()

• DEAReportGenerator$write_DEA_all()

• DEAReportGenerator$make_SummarizedExperiment()

• DEAReportGenerator$clone()

---

Method new()

Initialize DEAReportGenerator

Usage

DEAReportGenerator\$new(deanalyse, GRP2, name = "")

Arguments

deanalyse

DEAnalyse R6 object with completed analysis

GRP2

ProlfquAppConfig R6 object

name

optional name prefix for output files

---

Method prep_result_list()

Prepare result list with all analysis outputs for XLSX

Usage

DEAReportGenerator\$prep_result_list()

Returns

list containing all analysis results (14 sheets)

---

Method write_DEA()

Write DEA results (XLSX, ORA, GSEA files)

Usage

DEAReportGenerator\$write_DEA(ORA = TRUE, GSEA = TRUE)

Arguments

ORA

if TRUE write ORA gene lists

GSEA

if TRUE write GSEA rank files

Returns

list with xlsx_file, ora_files, gsea_files paths

---

Method make_boxplots()

Generate sample-level boxplots for quality control

Usage

DEAReportGenerator\$make_boxplots(boxplot = TRUE)

Arguments

boxplot

logical, if TRUE write boxplots

---

Method filter_data()

Get subset of transformed data for significant proteins

Usage

DEAReportGenerator\$filter_data()

---

Method get_protein_boxplots()

Get per-protein boxplots for significant proteins

Usage

DEAReportGenerator\$get_protein_boxplots()

---

Method contrasts_to_Grob()

Convert significant contrast results to table grobs. Column selection and rounding are driven by the contrast object’s ContrastConfiguration so SAINT and LM backends both produce grobs with canonical contrast/effect/ score/fdr columns without backend-specific code.

Usage

DEAReportGenerator\$contrasts_to_Grob()

---

Method get_protein_boxplots_contrasts()

Get per-protein boxplots combined with contrast summary tables

Usage

DEAReportGenerator\$get_protein_boxplots_contrasts()

---

Method write_protein_boxplots()

Write per-protein boxplots with contrast tables to PDF

Usage

DEAReportGenerator\$write_protein_boxplots(filename = "boxplots")

Arguments

filename

base filename (without extension)

---

Method write_DEA_all()

Write DEA data outputs: XLSX, ORA gene lists, GSEA rank files, and boxplots. HTML reports are rendered separately (Quarto) by ‘render_dea_reports()’.

Usage

DEAReportGenerator\$write_DEA_all(boxplot = TRUE, ORA = TRUE, GSEA = TRUE)

Arguments

boxplot

if TRUE generate boxplots

ORA

if TRUE write ORA gene lists

GSEA

if TRUE write GSEA rank files

Returns

list with ‘data_files’ paths; ‘dea_file’ / ‘qc_file’ are NULL as the Quarto reports are produced by ‘render_dea_reports()’

---

Method make_SummarizedExperiment()

Create SummarizedExperiment object from analysis results

Usage

DEAReportGenerator\$make_SummarizedExperiment(
  strip = "~lfq~light",
  .url_builder = prolfquapp::bfabric_url_builder
)

Arguments

strip

pattern to strip from rownames

.url_builder

function to build URLs for bfabric

Returns

SummarizedExperiment object

---

Method clone()

The objects of this class are cloneable with this method.

Usage

DEAReportGenerator\$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.