Merging of two tables containing search terms to expand search term database for the AnnotationBust function.

This function merges two data frames with search terms. This allows users to easily add search terms to data frames (either their own or ones included in this package using data() as GenBank annotations for the same genes may vary in gene name.

Usage

MergeSearchTerms(..., SortGenes = FALSE)

Arguments

...

the data frames of search terms you want to combine into a single data frame The Data frame(s) should have stringsAsFactors=FALSE listed if you want to sort them.

SortGenes

Should the final data frame be sorted by gene name? Default is FALSE.

Value

A new merged data frame with all the search terms combined from the lists supplied. If sort.gene=TRUE, genes will be sorted by name.

Examples

#load the list of search terms for mitochondrial genes
data(mtDNAterms) 

#Make a data.frame of new terms to add.
#This is a dummy example for a non-real annotation of COI, but lets pretend it is real.
add.name <- data.frame("COI","CDS", "CX1")

# make the column names the same for combination.
colnames(add.name) <- colnames(mtDNAterms)

#Run the merge search term function without sorting based on gene name.
new.terms <- MergeSearchTerms(add.name, mtDNAterms, SortGenes=FALSE)

#Run the merge search term function with sorting based on gene name.
new.terms <- MergeSearchTerms(add.name, mtDNAterms, SortGenes=TRUE)

#Merge search terms and create an additional column for introns and/or exons to extract
#In this example, add the trnK intron to the terms

###Example With matK CDS and addint introns/exons for trnK###
#Subset out matK from cpDNAterms
cds.terms <- subset(cpDNAterms,cpDNAterms$Feature=="matK")
#Create a vecotr of NA so we can merge with the search terms for introns and exons
cds.terms <- cbind(cds.terms,(rep(NA,length(cds.terms$Feature))))
colnames(cds.terms)[4] <- "IntronExonNumber"

#Prepare a search term table for the intron and exons to remove
#We can start with the cpDNAterms for trnK
IntronExon.terms<-subset(cpDNAterms,cpDNAterms$Feature=="trnK")

#As we want to go for two exons, we will want the synonyms repeated as we are doing and intron
#and an exon
IntronExon.terms<-rbind(IntronExon.terms,IntronExon.terms)#duplicate the terms

#rep the sequence type we want to extract
IntronExon.terms$Type <- rep(c("intron","intron","exon","exon"))
IntronExon.terms$Feature <- rep(c("trnK_Intron","trnK_Exon2"),each=2)
IntronExon.terms <- cbind(IntronExon.terms,rep(c(1,1,2,2)))#Add intron/exon number info

#change column name for number info for IntronExon name
colnames(IntronExon.terms)[4] <- "IntronExonNumber"

#We can then merge everything together with MergeSearchTerms terms
IntronExonExampleTerms <- MergeSearchTerms(IntronExon.terms,cds.terms)