forestPlot: Draw forest plot for differences betweeen cohorts.

Description Usage Arguments Details Value See Also Examples

View source: R/forestPlot.R

Description

Draw forest plot for differences betweeen cohorts.

Usage

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forestPlot(
  mafCompareRes,
  pVal = 0.05,
  fdr = NULL,
  color = NULL,
  geneFontSize = 1.2,
  titleSize = 1.2,
  lineWidth = 2.2
)

Arguments

mafCompareRes

results from mafCompare

pVal

p-value threshold. Default 0.05.

fdr

fdr threshold. Default NULL. If provided uses adjusted pvalues (fdr).

color

vector of colors for cohorts. Default NULL.

geneFontSize

Font size for gene symbols. Default 1.2

titleSize

font size for titles. Default 1.2

lineWidth

line width for CI bars. Default 2.2

Details

Plots results from link{mafCompare} as a forest plot with x-axis as log10 converted odds ratio and differentially mutated genes on y-axis.

Value

Nothing

See Also

mafCompare

Examples

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##Primary and Relapse APL
primary.apl <- system.file("extdata", "APL_primary.maf.gz", package = "maftools")
relapse.apl <- system.file("extdata", "APL_relapse.maf.gz", package = "maftools")
##Read mafs
primary.apl <- read.maf(maf = primary.apl)
relapse.apl <- read.maf(maf = relapse.apl)
##Perform analysis and draw forest plot.
pt.vs.rt <- mafCompare(m1 = primary.apl, m2 = relapse.apl, m1Name = 'Primary',
m2Name = 'Relapse', minMut = 5)
forestPlot(mafCompareRes = pt.vs.rt)

Example output

-Reading
-Validating
--Non MAF specific values in Variant_Classification column:
  ITD
-Silent variants: 45 
-Summarizing
-Processing clinical data
--Missing clinical data
-Finished in 0.421s elapsed (0.224s cpu) 
-Reading
-Validating
--Non MAF specific values in Variant_Classification column:
  ITD
-Silent variants: 19 
-Summarizing
-Processing clinical data
--Missing clinical data
-Finished in 0.159s elapsed (0.110s cpu) 

maftools documentation built on Feb. 6, 2021, 2 a.m.