toGRanges {ChIPpeakAnno} | R Documentation |
Convert UCSC BED format and its variants, such as GFF, or any user defined dataset such as RangedDate or MACS output file to GRanges
## S4 method for signature 'character' toGRanges(data, format=c("BED", "GFF", "MACS", "MACS2", "MACS2.broad", "narrowPeak", "broadPeak", "others"), header=FALSE, comment.char="#", colNames=NULL, ...) ## S4 method for signature 'connection' toGRanges(data, format=c("BED", "GFF", "MACS", "MACS2", "MACS2.broad", "narrowPeak", "broadPeak", "others"), header=FALSE, comment.char="#", colNames=NULL, ...) ## S4 method for signature 'data.frame' toGRanges(data, colNames=NULL, ...) ## S4 method for signature 'TxDb' toGRanges(data, feature=c("gene", "transcript", "exon", "CDS", "fiveUTR", "threeUTR", "microRNA", "tRNAs", "geneModel"), OrganismDb, ...) ## S4 method for signature 'EnsDb' toGRanges(data, feature=c("gene", "transcript", "exon", "disjointExons"), ...)
data |
an object of data.frame, TxDb or EnsDb, or the file name of data to be imported. Alternatively, data can be a readable txt-mode connection (See ?read.table). |
format |
data format. If the data format is set to BED, GFF, narrowPeak or broadPeak, please refer to http://genome.ucsc.edu/FAQ/FAQformat#format1 for column order. "MACS" is for converting the excel output file from MACS1. "MACS2" is for converting the output file from MACS2. |
feature |
annotation type |
header |
A logical value indicating whether the file contains the names of the variables as its first line. If missing, the value is determined from the file format: header is set to TRUE if and only if the first row contains one fewer field than the number of columns. |
comment.char |
character: a character vector of length one containing a single character or an empty string. Use "" to turn off the interpretation of comments altogether. |
colNames |
If the data format is set to "others", colname must be defined. And the colname must contain space, start and end. The column name for the chromosome # should be named as space. |
... |
parameters passed to read.table |
OrganismDb |
an object of OrganismDb. It is used for extracting gene symbol for geneModel group for TxDb |
An object of GRanges
Jianhong Ou
macs <- system.file("extdata", "MACS_peaks.xls", package="ChIPpeakAnno") macsOutput <- toGRanges(macs, format="MACS") if(Sys.getenv("USER")=="jianhongou"){ ## MACS connection macs <- readLines(macs) macs <- textConnection(macs) macsOutput <- toGRanges(macs, format="MACS") ## bed toGRanges(system.file("extdata", "MACS_output.bed", package="ChIPpeakAnno"), format="BED") ## narrowPeak toGRanges(system.file("extdata", "peaks.narrowPeak", package="ChIPpeakAnno"), format="narrowPeak") ## broadPeak toGRanges(system.file("extdata", "TAF.broadPeak", package="ChIPpeakAnno"), format="broadPeak") ## MACS2 toGRanges(system.file("extdata", "MACS2_peaks.xls", package="ChIPpeakAnno"), format="MACS2") ## GFF toGRanges(system.file("extdata", "GFF_peaks.gff", package="ChIPpeakAnno"), format="GFF") ## EnsDb library(EnsDb.Hsapiens.v75) toGRanges(EnsDb.Hsapiens.v75, feature="gene") ## TxDb library(TxDb.Hsapiens.UCSC.hg19.knownGene) toGRanges(TxDb.Hsapiens.UCSC.hg19.knownGene, feature="gene") ## data.frame macs <- system.file("extdata", "MACS_peaks.xls", package="ChIPpeakAnno") macs <- read.delim(macs, comment.char="#") toGRanges(macs) }