MMRFVariant_PlotVariantsbyGene: MMRFVariant_PlotVariantsbyGene

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

MMRFVariant_PlotVariantsbyGene

Description

draws heatmap of the annotated variants occurrences

Usage

MMRFVariant_PlotVariantsbyGene(
  variant.ann,
  ListGene = NULL,
  topN = 20,
  filenm = "PlotVariantsbyGene_heatmap",
  height = 10,
  width = 10
)

Arguments

variant.ann	is the dataframe of annotated variants downloaded from MMRF-Commpass Researcher Gateway (i.e. MMRF_CoMMpass_IA14a_All_Canonical_Variants file) and imported into environment
ListGene	is the list of the genes to analyze (optional).
topN	is the top number of genes whose to visualize the variants occurrence number
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

Value

heatmap of the annotated variants occurrences

Examples

variant.ann<- data.frame(public_id=c("MMRF_0000","MMRF_0001",
                                     "MMRF_0002","MMRF_0003",
                                     "MMRF_0004","MMRF_0005",
                                     "MMRF_0006","MMRF_0007",
                                     "MMRF_0008",""),                  
                 dbSNP=c(rep("rs755588843",2),rep("rs569344016",5),rep("rs2066497",2),rep(".",1)),                                                    
                 Effect=c(rep("intragenic_variant",3),
                           rep("missense_variant",2),
                           rep("intron_variant",1),
                           rep("5_prime_UTR_variant",4)),
                  Gene=c(rep("PRDM16",3),
                           rep("AGO1",2),
                           rep("FPGT-TNNI3K",1),
                           rep("TNNI3K",4)), 
                 REF=c(rep("C",3),
                           rep("G",2),
                           rep("A",1),
                           rep("T",4)),                            
                 ALT=c(rep("GGCCT",3),
                           rep("G",2),
                           rep("T",1),
                           rep("A",4)),    
                  Biotype=c(rep("protein_coding",6),
                           rep("antisense",2),
                           rep("processed_pseudogene",2)),   
                           
                 Impact= c(rep("MODERATE",2),rep("MODIFIER",2),
                            rep("LOW",3),rep("HIGH",2),rep("MODIFIER",1)),
                 feature_type= c(rep("ENST00000388718",2),rep("ENST00000344616",2),
                            rep("ENST00000431492",3),rep("ENST00000390268",2),rep("ENST00000316407",1)),
                            
                 SIFT= c(rep("0.035,0.035,0.057,0.057,0.035,0.042,0.04,0.058",2),rep("0.002,0.002,0.001,0.002",2),
                            rep("0.614,0.614,0.781",6)),           
                            
                 Polyphen2=c(rep("0.021,0.986,0.884,0.977",2),rep("0.99",2),
                            rep("0.614,0.781",6))           
                                                              
                                 
 )





variants.plot<-MMRFVariant_PlotVariantsbyGene(variant.ann,ListGene,topN=10,)
variants.plot<-MMRFVariant_PlotVariantsbyGene(variant.ann,topN=10)

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