hi all -- does anyone know how to turn off the forced conversion of character vectors to factors when merging with IRanges::DataFrame objects? in the example below fooX.df is a base data.frame, while fooX.DF is the IRanges::DataFrame equivalent. example: > foo1.df <- data.frame(a = letters[1:10], b = runif(10), stringsAsFactors = FALSE); foo1.DF <- DataFrame(foo1.df) > foo2.df <- data.frame(a = letters[1:10], c = -runif(10), stringsAsFactors = FALSE); foo2.DF <- DataFrame(foo2.df) > foo3.df <- merge(foo1.df, foo2.df); foo3.DF <- merge(foo1.DF, foo2.DF) > sapply(foo3.df, class); foo3.df a b c "character" "numeric" "numeric" a b c 1 a 0.4112609 -0.64623114 2 b 0.5656937 -0.88098189 3 c 0.4682333 -0.26826974 4 d 0.1374115 -0.05801876 5 e 0.3506727 -0.23886691 6 f 0.5035583 -0.14777341 7 g 0.6833072 -0.09146686 8 h 0.7256269 -0.20445511 9 i 0.9553401 -0.76399925 10 j 0.3809191 -0.66888397 > sapply(foo3.DF, class); foo3.DF a b c "factor" "numeric" "numeric" DataFrame with 10 rows and 3 columns a b c <factor> <numeric> <numeric> 1 a 0.4112609 -0.64623114 2 b 0.5656937 -0.88098189 3 c 0.4682333 -0.26826974 4 d 0.1374115 -0.05801876 5 e 0.3506727 -0.23886691 6 f 0.5035583 -0.14777341 7 g 0.6833072 -0.09146686 8 h 0.7256269 -0.20445511 9 i 0.9553401 -0.76399925 10 j 0.3809191 -0.66888397 i've tried adding the "stringsAsFactors = FALSE" into the merge(...) calls, thinking perhaps that switch is forwarded to an underlying data.frame(...) call, but that doesn't seem to the be the case (as "a" is still converted to a factor). i'd also rather not turn off the global stringsAsFactors behavior, as i want to ensure my script runs properly on others' R setups without having to modify their state. thanks for any help! -murat

I went in and cleaned a lot of this up. We now no longer coerce strings to factors when coercing a DataFrame to data.frame, nor do we check column names. Version: 1.19.25 On Tue, Aug 20, 2013 at 11:18 AM, Murat Tasan <mmuurr@gmail.com> wrote: > hi all -- does anyone know how to turn off the forced conversion of > character vectors to factors when merging with IRanges::DataFrame > objects? > in the example below fooX.df is a base data.frame, while fooX.DF is > the IRanges::DataFrame equivalent. > > example: > > > foo1.df <- data.frame(a = letters[1:10], b = runif(10), stringsAsFactors > = FALSE); foo1.DF <- DataFrame(foo1.df) > > foo2.df <- data.frame(a = letters[1:10], c = -runif(10), > stringsAsFactors = FALSE); foo2.DF <- DataFrame(foo2.df) > > foo3.df <- merge(foo1.df, foo2.df); foo3.DF <- merge(foo1.DF, foo2.DF) > > sapply(foo3.df, class); foo3.df > a b c > "character" "numeric" "numeric" > a b c > 1 a 0.4112609 -0.64623114 > 2 b 0.5656937 -0.88098189 > 3 c 0.4682333 -0.26826974 > 4 d 0.1374115 -0.05801876 > 5 e 0.3506727 -0.23886691 > 6 f 0.5035583 -0.14777341 > 7 g 0.6833072 -0.09146686 > 8 h 0.7256269 -0.20445511 > 9 i 0.9553401 -0.76399925 > 10 j 0.3809191 -0.66888397 > > sapply(foo3.DF, class); foo3.DF > a b c > "factor" "numeric" "numeric" > DataFrame with 10 rows and 3 columns > a b c > <factor> <numeric> <numeric> > 1 a 0.4112609 -0.64623114 > 2 b 0.5656937 -0.88098189 > 3 c 0.4682333 -0.26826974 > 4 d 0.1374115 -0.05801876 > 5 e 0.3506727 -0.23886691 > 6 f 0.5035583 -0.14777341 > 7 g 0.6833072 -0.09146686 > 8 h 0.7256269 -0.20445511 > 9 i 0.9553401 -0.76399925 > 10 j 0.3809191 -0.66888397 > > > i've tried adding the "stringsAsFactors = FALSE" into the merge(...) > calls, thinking perhaps that switch is forwarded to an underlying > data.frame(...) call, but that doesn't seem to the be the case (as "a" > is still converted to a factor). > i'd also rather not turn off the global stringsAsFactors behavior, as > i want to ensure my script runs properly on others' R setups without > having to modify their state. > > thanks for any help! > > -murat > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]