In marziasettino/MMRFVariant: R package for variant analysis from MMRF-CoMMpass data source

knitr::opts_chunk$set(
  collapse = TRUE,
  warning=FALSE, 
  message=FALSE,
  comment = "#>"
)

MMRFVariant_GetVariantsbyGene

Arguments | Description -----|----- variant.ann| is the data.frame of the annotated variants downloaded from MMRF-Commpass Researcher Gateway ListGene| is the list of the genes to analyze

Example

variants.list<-MMRFVariant_GetVariantsbyGene(variant.ann, ListGene)

MMRFVariant_PlotVariantsbyGene

Arguments | Description -----|----- variant.ann| is the data.frame of the annotated variants downloaded from MMRF-Commpass Researcher Gateway ListGene| is the list of the genes to analyze topN| is the top number of variant count to visualize filenm| is the name of the png file. If filenm is Null, the plot is draw but it is not saved height| Image height width| Image width

Example

variants.plot<-MMRFVariant_PlotVariantsbyGene(variant.ann, ListGene)

MMRFVariant_PlotbyEffectImpact

Arguments | Description -----|----- variant.ann| is the data.frame of the annotated variants downloaded from MMRF-Commpass Researcher Gateway ListSNP| is the list of the SNPs to analyze. topN| is the top number of variant count to visualize filenm| is the name of the png file. If filenm is Null, the plot is draw but it is not saved height| Image height width| Image width

Example

summary.plot<-MMRFVariant_PlotbyEffectImpact(variant.ann,topN=50,height=10, width=15, filenm="PlotbyEffect")

marziasettino/MMRFVariant documentation built on March 28, 2023, 3:16 p.m.