## ----include=FALSE------------------------------------------------------------ library(BiocStyle) ## ----------------------------------------------------------------------------- library(scanMiRApp) # we create a temporary directory in which the files will be saved tmp <- tempdir() f <- file.path(tmp, "test") # we create a dummy data.frame d <- data.frame( category=sample(LETTERS[1:4], 10000, replace=TRUE), var2=sample(LETTERS, 10000, replace=TRUE), var3=runif(10000) ) saveIndexedFst(d, index.by="category", file.prefix=f) ## ----------------------------------------------------------------------------- d2 <- loadIndexedFst(f) class(d2) summary(d2) ## ----------------------------------------------------------------------------- format(object.size(d),units="Kb") format(object.size(d2),units="Kb") ## ----------------------------------------------------------------------------- nrow(d2) ncol(d2) colnames(d2) head(d2) ## ----------------------------------------------------------------------------- names(d2) lengths(d2) ## ----------------------------------------------------------------------------- catB <- d2$B head(catB) ## ----------------------------------------------------------------------------- library(GenomicRanges) gr <- GRanges(sample(LETTERS[1:3],200,replace=TRUE), IRanges(seq_len(200), width=2)) gr$propertyA <- factor(sample(letters[1:5],200,replace=TRUE)) gr ## ----------------------------------------------------------------------------- f2 <- file.path(tmp, "test2") saveIndexedFst(gr, index.by="seqnames", file.prefix=f2) d1 <- loadIndexedFst(f2) names(d1) head(d1$A) ## ----------------------------------------------------------------------------- saveIndexedFst(gr, index.by="propertyA", file.prefix=f2) d2 <- loadIndexedFst(f2) names(d2) ## ----------------------------------------------------------------------------- list.files(tmp, "test2") ## ----sessionInfo, echo=FALSE-------------------------------------------------- sessionInfo()