KYCG_plotManhattan: KYCG_plotManhattan makes a manhattan plot to summarize EWAS...

In zwdzwd/sesame: SEnsible Step-wise Analysis of DNA MEthylation BeadChips

KYCG_plotManhattan makes a manhattan plot to summarize EWAS results

Description

KYCG_plotManhattan makes a manhattan plot to summarize EWAS results

Usage

KYCG_plotManhattan(
  vals,
  platform = NULL,
  genome = NULL,
  title = NULL,
  label_min = 100,
  col = c("wheat1", "sienna3"),
  ylabel = "Value"
)

Arguments

vals	named vector of values (P,Q etc), vector name is Probe ID.
platform	String corresponding to the type of platform to use for retrieving GRanges coordinates of probes. Either MM285, EPIC, HM450, or HM27. If it is not provided, it will be inferred from the query set probeIDs (Default: NA).
genome	hg38, mm10, ..., will infer if not given. For additional mapping, download the GRanges object from http://zwdzwd.github.io/InfiniumAnnotation and provide the following argument ..., genome = sesameAnno_buildManifestGRanges("downloaded_file"),... to this function.
title	title for plot
label_min	Threshold above which data points will be labelled with Probe ID
col	color
ylabel	y-axis label

Value

a ggplot object

Examples

## see vignette for examples
sesameDataGet_resetEnv()

zwdzwd/sesame documentation built on April 28, 2024, 12:48 p.m.