DEAReportGenerator

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$render_DEA()

• DEAReportGenerator$make_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 render_DEA()

Render DEA report using R Markdown

Usage

DEAReportGenerator$render_DEA(
  htmlname,
  markdown = "_Grp2Analysis_V2_R6.Rmd",
  word = FALSE,
  toc = TRUE
)

Arguments

htmlname

name for the output HTML file

markdown

path to the R Markdown template file

word

logical, if TRUE output Word document, otherwise HTML

toc

logical, if TRUE include table of contents

Returns

path to the output file

---

Method make_boxplots()

Generate boxplots for quality control

Usage

DEAReportGenerator$make_boxplots(boxplot = TRUE)

Arguments

boxplot

logical, if TRUE write boxplots

---

Method write_DEA_all()

Write all DEA results: XLSX, ORA, GSEA, HTML reports, boxplots

Usage

DEAReportGenerator$write_DEA_all(
  boxplot = TRUE,
  render = TRUE,
  ORA = TRUE,
  GSEA = TRUE,
  markdown = "_Grp2Analysis_V2_R6.Rmd",
  markdown_qc = "_DiffExpQC_R6.Rmd",
  toc = TRUE
)

Arguments

boxplot

if TRUE generate boxplots

render

if TRUE render HTML reports

ORA

if TRUE write ORA gene lists

GSEA

if TRUE write GSEA rank files

markdown

Rmd template for main DEA report

markdown_qc

Rmd template for QC report

toc

if TRUE include table of contents

Returns

list with dea_file, qc_file, data_files paths

---

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.