render_report: Build report for TCGA.pipe function

In ELMER: Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

Description

Build HTML report

Usage

render_report(
  title = "Report",
  mae,
  group.col,
  group1,
  group2,
  direction,
  dir.out,
  genome = "hg38",
  mode = "supervised",
  minSubgroupFrac = "20%",
  minMetdiff = "0.3",
  metfdr = "0.01",
  permu = "10000",
  rawpval = "0.01",
  pe = "0.01",
  nprobes = "10",
  lower.OR = "1.1",
  out_file = file.path(getwd(), "report.html")
)

Arguments

title	HTML report title
mae	Absolute path to the mae used in the analysis
group.col	Group col
group1	Group 1
group2	Group 2
direction	direction used in the analysis
dir.out	Absolute path to folder with results. dir.out used in the analysis
genome	Genome of reference used in the analysis
mode	mode used in the analysis
minSubgroupFrac	minSubgroupFrac used in the analysis
minMetdiff	minMetdiff used in the analysis
metfdr	metfdr used in the analysis
permu	permu used in the analysis
rawpval	rawpval used in the analysis
pe	pe used in the analysis
nprobes	nprobes used in the analysis
lower.OR	lower.OR used in the analysis
out_file	Output file name (i.e report.html)

Examples

## Not run: 
render_report(group.col = "TN",
              group1 = "Tumor",
              group2 = "Normal",
              dir.out = "~/paper_elmer/Result/BRCA/TN_Tumor_vs_Normal/hypo/",
              direction = "hypo",
              mae = "~/paper_elmer/Result/BRCA/BRCA_mae_hg38.rda")

## End(Not run)

ELMER documentation built on Nov. 8, 2020, 4:59 p.m.