RankView {MAGeCKFlute}R Documentation

View the rank of gene points

Description

Rank all genes according to beta score deviation, and label top and bottom meaningful genes. Some other interested genes can be labeled too.

Usage

RankView(rankdata, genelist = NA, top = 20, bottom = 20,
  cutoff = c(-sd(rankdata), sd(rankdata)), main = NULL,
  filename = NULL, width = 5, height = 4, ...)

Arguments

rankdata

Numeric vector, with gene as names.

genelist

Character vector, specifying genes to be labeled in figure.

top

Integer, specifying number of top genes to be labeled.

bottom

Integer, specifying number of bottom genes to be labeled.

cutoff

A two-length numeric vector, in which first value is bottom cutoff, and second value is top cutoff.

main

As in 'plot'.

filename

Figure file name to create on disk. Default filename="NULL", which means no output.

width

As in ggsave.

height

As in ggsave.

...

Other available parameters in function 'ggsave'.

Value

An object created by ggplot, which can be assigned and further customized.

Author(s)

Wubing Zhang

Examples

data(rra.gene_summary)
rra = ReadRRA(rra.gene_summary, organism = "hsa")
rankdata = rra$LFC
names(rankdata) = rra$Official
RankView(rankdata)


[Package MAGeCKFlute version 1.2.3 Index]