export_gmql {RGMQL} | R Documentation |
It creates GMQL dataset from GRangesList. All samples are in GDM (tab-separated values) or GTF file format
export_gmql(samples, dir_out, is_gtf)
samples |
GRangesList |
dir_out |
folder path where to create a folder and write the sample files |
is_gtf |
logical value indicating if samples have to be exported with GTF or GDM format |
The GMQL dataset is made up by two different file types:
metadata files: they contain metadata associated with corrisponding sample.
region files: they contain genomic regions data.
region schema file: XML file that contains region attribute names (e.g. chr, start, end, pvalue)
Sample region files and metadata files are associated through file name: for example S_0001.gdm for region file and S_0001.gdm.meta for its metadata file
None
## Load and attach add-on GenomicRanges package library(GenomicRanges) ## These statemens create two GRanges with the region attributes: seqnames, ## ranges (region coordinates) and strand, plus two column elements: ## score and GC gr1 <- GRanges(seqnames = "chr2", ranges = IRanges(3, 6), strand = "+", score = 5L, GC = 0.45) gr2 <- GRanges(seqnames = c("chr1", "chr1"), ranges = IRanges(c(7,13), width = 3), strand = c("+", "-"), score = 3:4, GC = c(0.3, 0.5)) ## This statement creates a GRangesList using the previous GRanges grl = GRangesList(gr1, gr2) ## This statement defines the path to the subdirectory "example" of the ## package "RGMQL" and exports the GRangesList as GMQL datasets with sample ## files in GTF file format, using the last name of 'dir_out' path as ## dataset name test_out_path <- system.file("example", package = "RGMQL") export_gmql(grl, test_out_path, TRUE)