MMRFVariant_GetVariantsbyGene: MMRFVariant_GetVariantsbyGene

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

MMRFVariant_GetVariantsbyGene

Description

get variants occurring in a gene set provided as input

Usage

MMRFVariant_GetVariantsbyGene(variant.ann, ListGene = NULL)

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. if it is Null, the list of variants oredere by the occurrence nuomber is shown

Value

the list of SNPs found in the gene list provided as input

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

variants.list<-MMRFVariant_GetVariantsbyGene(variant.ann)

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