How to use a string as an environment name in mget?
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Jarno Tuimala ▴ 140
@jarno-tuimala-1650
Last seen 10.2 years ago
Dear all, Is it possible to use a string as an environment name in mget? I was trying to do this with the following script, but it says that the second argument for mget is not an environment. Well, I know it isn't, since it was generated using paste function, so it's class is character. > genes<-c("1007_s_at", "1053_at", "117_at", "121_at") > chip<-"hgu133a" > library(package=chip, character.only=T) > env<-paste(chip, "REFSEQ", sep="") > refseq<-as.vector(unlist(mget(genes, envir=env))) Error in mget(x, envir, mode, ifnotfound, inherits) : second argument must be an environment The following works fine: > refseq<-as.vector(unlist(mget(genes, envir=hgu133aREFSEQ))) But, I'm trying to put together a script I could easily just source for different datasets, so I would like to avoid typing the name of the environment every time (I read the name of the Affymetrix chip set from a second file in the actual script). Best regards, Jarno Tuimala
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@wolfgang-huber-3550
Last seen 3 months ago
EMBL European Molecular Biology Laborat…
Hi, get(env) will be an environment if env is the name of an environment. Best wishes Wolfgang ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber Jarno Tuimala wrote: > Dear all, > > Is it possible to use a string as an environment name in mget? I was > trying to do this with the following script, but it says that the second > argument for mget is not an environment. Well, I know it isn't, since it > was generated using paste function, so it's class is character. > >> genes<-c("1007_s_at", "1053_at", "117_at", "121_at") >> chip<-"hgu133a" >> library(package=chip, character.only=T) >> env<-paste(chip, "REFSEQ", sep="") >> refseq<-as.vector(unlist(mget(genes, envir=env))) > Error in mget(x, envir, mode, ifnotfound, inherits) : > second argument must be an environment > > The following works fine: > >> refseq<-as.vector(unlist(mget(genes, envir=hgu133aREFSEQ))) > > But, I'm trying to put together a script I could easily just source for > different datasets, so I would like to avoid typing the name of the > environment every time (I read the name of the Affymetrix chip set from a > second file in the actual script). > > Best regards, > Jarno Tuimala
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