Important Data Objects for Range Operations
IRanges: stores range data only (IRanges library)GRanges: stores ranges and annotations (GenomicRanges library)GRangesList: list version of GRanges container (GenomicRanges library)
Range Data Are Stored in IRanges and GRanges Containers
Construct GRanges Object
library(GenomicRanges); library(rtracklayer)
gr <- GRanges(seqnames = Rle(c("chr1", "chr2", "chr1", "chr3"), c(1, 3, 2, 4)), ranges = IRanges(1:10, end = 7:16, names = head(letters, 10)), strand = Rle(strand(c("-", "+", "*", "+", "-")), c(1, 2, 2, 3, 2)), score = 1:10, GC = seq(1, 0, length = 10)) # Example of creating a GRanges object with its constructor function.
Import GFF into GRanges Object
gff <- import.gff("http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/Samples/gff3.gff") # Imports a simplified GFF3 genome annotation file.
seqlengths(gff) <- end(ranges(gff[which(values(gff)[,"type"]=="chromosome"),]))
names(gff) <- 1:length(gff) # Assigns names to corresponding slot
gff[1:4,]
## GRanges object with 4 ranges and 10 metadata columns:
## seqnames ranges strand | source type score phase ID
## <Rle> <IRanges> <Rle> | <factor> <factor> <numeric> <integer> <character>
## 1 Chr1 [ 1, 30427671] + | TAIR10 chromosome <NA> <NA> Chr1
## 2 Chr1 [3631, 5899] + | TAIR10 gene <NA> <NA> AT1G01010
## 3 Chr1 [3631, 5899] + | TAIR10 mRNA <NA> <NA> AT1G01010.1
## 4 Chr1 [3760, 5630] + | TAIR10 protein <NA> <NA> AT1G01010.1-Protein
## Name Note Parent Index Derives_from
## <character> <CharacterList> <CharacterList> <character> <character>
## 1 Chr1 <NA> <NA>
## 2 AT1G01010 protein_coding_gene <NA> <NA>
## 3 AT1G01010.1 AT1G01010 1 <NA>
## 4 AT1G01010.1 <NA> AT1G01010.1
## -------
## seqinfo: 7 sequences from an unspecified genome
Coerce GRanges object to data.frame
as.data.frame(gff)[1:4, 1:7]
## seqnames start end width strand source type
## 1 Chr1 1 30427671 30427671 + TAIR10 chromosome
## 2 Chr1 3631 5899 2269 + TAIR10 gene
## 3 Chr1 3631 5899 2269 + TAIR10 mRNA
## 4 Chr1 3760 5630 1871 + TAIR10 protein
Coerce GRanges to RangedData object and vice versa
gff_rd <- as(gff, "RangedData")
gff_gr <- as(gff_rd, "GRanges")
Utilities for Range Containers
Accessor and subsetting methods for GRanges objects
Subsetting and replacement
gff[1:4]
## GRanges object with 4 ranges and 10 metadata columns:
## seqnames ranges strand | source type score phase ID
## <Rle> <IRanges> <Rle> | <factor> <factor> <numeric> <integer> <character>
## 1 Chr1 [ 1, 30427671] + | TAIR10 chromosome <NA> <NA> Chr1
## 2 Chr1 [3631, 5899] + | TAIR10 gene <NA> <NA> AT1G01010
## 3 Chr1 [3631, 5899] + | TAIR10 mRNA <NA> <NA> AT1G01010.1
## 4 Chr1 [3760, 5630] + | TAIR10 protein <NA> <NA> AT1G01010.1-Protein
## Name Note Parent Index Derives_from
## <character> <CharacterList> <CharacterList> <character> <character>
## 1 Chr1 <NA> <NA>
## 2 AT1G01010 protein_coding_gene <NA> <NA>
## 3 AT1G01010.1 AT1G01010 1 <NA>
## 4 AT1G01010.1 <NA> AT1G01010.1
## -------
## seqinfo: 7 sequences from an unspecified genome
gff[1:4, c("type", "ID")]
## GRanges object with 4 ranges and 2 metadata columns:
## seqnames ranges strand | type ID
## <Rle> <IRanges> <Rle> | <factor> <character>
## 1 Chr1 [ 1, 30427671] + | chromosome Chr1
## 2 Chr1 [3631, 5899] + | gene AT1G01010
## 3 Chr1 [3631, 5899] + | mRNA AT1G01010.1
## 4 Chr1 [3760, 5630] + | protein AT1G01010.1-Protein
## -------
## seqinfo: 7 sequences from an unspecified genome
gff[2] <- gff[3]
GRanges objects can be concatenated with the c function
c(gff[1:2], gff[401:402])
## GRanges object with 4 ranges and 10 metadata columns:
## seqnames ranges strand | source type score phase
## <Rle> <IRanges> <Rle> | <factor> <factor> <numeric> <integer>
## 1 Chr1 [ 1, 30427671] + | TAIR10 chromosome <NA> <NA>
## 2 Chr1 [3631, 5899] + | TAIR10 mRNA <NA> <NA>
## 401 Chr5 [5516, 5769] - | TAIR10 protein <NA> <NA>
## 402 Chr5 [5770, 5801] - | TAIR10 five_prime_UTR <NA> <NA>
## ID Name Note Parent Index Derives_from
## <character> <character> <CharacterList> <CharacterList> <character> <character>
## 1 Chr1 Chr1 <NA> <NA>
## 2 AT1G01010.1 AT1G01010.1 AT1G01010 1 <NA>
## 401 AT5G01015.2-Protein AT5G01015.2 <NA> AT5G01015.2
## 402 <NA> <NA> AT5G01015.2 <NA> <NA>
## -------
## seqinfo: 7 sequences from an unspecified genome
Acessor functions
seqnames(gff)
## factor-Rle of length 449 with 7 runs
## Lengths: 72 22 38 118 172 13 14
## Values : Chr1 Chr2 Chr3 Chr4 Chr5 ChrC ChrM
## Levels(7): Chr1 Chr2 Chr3 Chr4 Chr5 ChrC ChrM
ranges(gff)
## IRanges of length 449
## start end width names
## [1] 1 30427671 30427671 1
## [2] 3631 5899 2269 2
## [3] 3631 5899 2269 3
## [4] 3760 5630 1871 4
## [5] 3631 3913 283 5
## ... ... ... ... ...
## [445] 11918 12241 324 445
## [446] 11918 12241 324 446
## [447] 11918 12241 324 447
## [448] 11918 12241 324 448
## [449] 11918 12241 324 449
strand(gff)
## factor-Rle of length 449 with 13 runs
## Lengths: 18 54 28 21 12 117 1 171 1 12 1 8 5
## Values : + - + - + - + - + - + - +
## Levels(3): + - *
seqlengths(gff)
## Chr1 Chr2 Chr3 Chr4 Chr5 ChrC ChrM
## 30427671 19698289 23459830 18585056 26975502 154478 366924
start(gff[1:4])
## [1] 1 3631 3631 3760
end(gff[1:4])
## [1] 30427671 5899 5899 5630
width(gff[1:4])
## [1] 30427671 2269 2269 1871
Accessing metadata component
values(gff) # or elementMetadata(gff)
## DataFrame with 449 rows and 10 columns
## source type score phase ID Name Note
## <factor> <factor> <numeric> <integer> <character> <character> <CharacterList>
## 1 TAIR10 chromosome NA NA Chr1 Chr1
## 2 TAIR10 mRNA NA NA AT1G01010.1 AT1G01010.1
## 3 TAIR10 mRNA NA NA AT1G01010.1 AT1G01010.1
## 4 TAIR10 protein NA NA AT1G01010.1-Protein AT1G01010.1
## 5 TAIR10 exon NA NA NA NA
## ... ... ... ... ... ... ... ...
## 445 TAIR10 gene NA NA ATMG00030 ATMG00030 protein_coding_gene
## 446 TAIR10 mRNA NA NA ATMG00030.1 ATMG00030.1
## 447 TAIR10 protein NA NA ATMG00030.1-Protein ATMG00030.1
## 448 TAIR10 exon NA NA NA NA
## 449 TAIR10 CDS NA 0 NA NA
## Parent Index Derives_from
## <CharacterList> <character> <character>
## 1 NA NA
## 2 AT1G01010 1 NA
## 3 AT1G01010 1 NA
## 4 NA AT1G01010.1
## 5 AT1G01010.1 NA NA
## ... ... ... ...
## 445 NA NA
## 446 ATMG00030 1 NA
## 447 NA ATMG00030.1
## 448 ATMG00030.1 NA NA
## 449 ATMG00030.1,ATMG00030.1-Protein NA NA
values(gff)[, "type"][1:20]
## [1] chromosome mRNA mRNA protein exon five_prime_UTR
## [7] CDS exon CDS exon CDS exon
## [13] CDS exon CDS exon CDS three_prime_UTR
## [19] gene mRNA
## Levels: chromosome gene mRNA protein exon five_prime_UTR CDS three_prime_UTR rRNA tRNA
gff[elementMetadata(gff)[ ,"type"] == "gene"]
## GRanges object with 21 ranges and 10 metadata columns:
## seqnames ranges strand | source type score phase ID
## <Rle> <IRanges> <Rle> | <factor> <factor> <numeric> <integer> <character>
## 19 Chr1 [ 5928, 8737] - | TAIR10 gene <NA> <NA> AT1G01020
## 64 Chr1 [11649, 13714] - | TAIR10 gene <NA> <NA> AT1G01030
## 74 Chr2 [ 1025, 2810] + | TAIR10 gene <NA> <NA> AT2G01008
## 84 Chr2 [ 3706, 5513] + | TAIR10 gene <NA> <NA> AT2G01010
## 87 Chr2 [ 5782, 5945] + | TAIR10 gene <NA> <NA> AT2G01020
## ... ... ... ... ... ... ... ... ... ...
## 427 ChrC [ 383, 1444] - | TAIR10 gene <NA> <NA> ATCG00020
## 432 ChrC [ 1717, 4347] - | TAIR10 gene <NA> <NA> ATCG00030
## 437 ChrM [ 273, 734] - | TAIR10 gene <NA> <NA> ATMG00010
## 442 ChrM [ 8848, 11415] - | TAIR10 gene <NA> <NA> ATMG00020
## 445 ChrM [11918, 12241] + | TAIR10 gene <NA> <NA> ATMG00030
## Name Note Parent Index Derives_from
## <character> <CharacterList> <CharacterList> <character> <character>
## 19 AT1G01020 protein_coding_gene <NA> <NA>
## 64 AT1G01030 protein_coding_gene <NA> <NA>
## 74 AT2G01008 protein_coding_gene <NA> <NA>
## 84 AT2G01010 rRNA <NA> <NA>
## 87 AT2G01020 rRNA <NA> <NA>
## ... ... ... ... ... ...
## 427 ATCG00020 protein_coding_gene <NA> <NA>
## 432 ATCG00030 tRNA <NA> <NA>
## 437 ATMG00010 protein_coding_gene <NA> <NA>
## 442 ATMG00020 rRNA <NA> <NA>
## 445 ATMG00030 protein_coding_gene <NA> <NA>
## -------
## seqinfo: 7 sequences from an unspecified genome
Useful utilities for GRanges objects
Remove chromosome ranges
gff <- gff[values(gff)$type != "chromosome"]
Erase the strand information
strand(gff) <- "*"
Collapses overlapping ranges to continuous ranges.
reduce(gff)
## GRanges object with 22 ranges and 0 metadata columns:
## seqnames ranges strand
## <Rle> <IRanges> <Rle>
## [1] Chr1 [ 3631, 5899] *
## [2] Chr1 [ 5928, 8737] *
## [3] Chr1 [11649, 13714] *
## [4] Chr2 [ 1025, 2810] *
## [5] Chr2 [ 3706, 5513] *
## ... ... ... ...
## [18] ChrC [ 383, 1444] *
## [19] ChrC [ 1717, 4347] *
## [20] ChrM [ 273, 734] *
## [21] ChrM [ 8848, 11415] *
## [22] ChrM [11918, 12241] *
## -------
## seqinfo: 7 sequences from an unspecified genome
Return uncovered regions
gaps(gff)
## GRanges object with 43 ranges and 0 metadata columns:
## seqnames ranges strand
## <Rle> <IRanges> <Rle>
## [1] Chr1 [ 1, 30427671] +
## [2] Chr1 [ 1, 30427671] -
## [3] Chr1 [ 1, 3630] *
## [4] Chr1 [5900, 5927] *
## [5] Chr1 [8738, 11648] *
## ... ... ... ...
## [39] ChrM [ 1, 366924] -
## [40] ChrM [ 1, 272] *
## [41] ChrM [ 735, 8847] *
## [42] ChrM [11416, 11917] *
## [43] ChrM [12242, 366924] *
## -------
## seqinfo: 7 sequences from an unspecified genome
Return disjoint ranges
disjoin(gff)
## GRanges object with 211 ranges and 0 metadata columns:
## seqnames ranges strand
## <Rle> <IRanges> <Rle>
## [1] Chr1 [3631, 3759] *
## [2] Chr1 [3760, 3913] *
## [3] Chr1 [3914, 3995] *
## [4] Chr1 [3996, 4276] *
## [5] Chr1 [4277, 4485] *
## ... ... ... ...
## [207] ChrC [ 1752, 4310] *
## [208] ChrC [ 4311, 4347] *
## [209] ChrM [ 273, 734] *
## [210] ChrM [ 8848, 11415] *
## [211] ChrM [11918, 12241] *
## -------
## seqinfo: 7 sequences from an unspecified genome
Returns coverage of ranges
coverage(gff)
## RleList of length 7
## $Chr1
## integer-Rle of length 30427671 with 45 runs
## Lengths: 3630 129 154 82 281 ... 233 161 380 30413957
## Values : 0 4 5 3 5 ... 4 2 4 0
##
## $Chr2
## integer-Rle of length 19698289 with 14 runs
## Lengths: 1024 248 185 53 362 ... 164 625 102 19691617
## Values : 0 5 3 5 3 ... 3 0 5 0
##
## $Chr3
## integer-Rle of length 23459830 with 29 runs
## Lengths: 1652 145 139 111 95 ... 155 148 156 23453781
## Values : 0 4 5 3 5 ... 3 5 4 0
##
## $Chr4
## integer-Rle of length 18585056 with 72 runs
## Lengths: 1179 357 1358 128 872 ... 212 114 74 18571697
## Values : 0 5 0 5 3 ... 3 5 4 0
##
## $Chr5
## integer-Rle of length 26975502 with 64 runs
## Lengths: 1222 28 28 109 72 ... 76 55 174 26967058
## Values : 0 4 7 13 16 ... 3 5 4 0
##
## ...
## <2 more elements>
Return the index pairings for overlapping ranges
findOverlaps(gff, gff[1:4])
## Hits object with 55 hits and 0 metadata columns:
## queryHits subjectHits
## <integer> <integer>
## [1] 1 1
## [2] 1 2
## [3] 1 4
## [4] 1 3
## [5] 2 1
## ... ... ...
## [51] 16 1
## [52] 16 2
## [53] 16 3
## [54] 17 1
## [55] 17 2
## -------
## queryLength: 442
## subjectLength: 4
Counts overlapping ranges
countOverlaps(gff, gff[1:4])[1:40]
## 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34
## 4 4 4 4 3 4 3 3 3 3 3 3 3 3 3 3 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## 35 36 37 38 39 40 41
## 0 0 0 0 0 0 0
Return only overlapping ranges
subsetByOverlaps(gff, gff[1:4])
## GRanges object with 17 ranges and 10 metadata columns:
## seqnames ranges strand | source type score phase
## <Rle> <IRanges> <Rle> | <factor> <factor> <numeric> <integer>
## 2 Chr1 [3631, 5899] * | TAIR10 mRNA <NA> <NA>
## 3 Chr1 [3631, 5899] * | TAIR10 mRNA <NA> <NA>
## 4 Chr1 [3760, 5630] * | TAIR10 protein <NA> <NA>
## 5 Chr1 [3631, 3913] * | TAIR10 exon <NA> <NA>
## 6 Chr1 [3631, 3759] * | TAIR10 five_prime_UTR <NA> <NA>
## ... ... ... ... ... ... ... ... ...
## 14 Chr1 [5174, 5326] * | TAIR10 exon <NA> <NA>
## 15 Chr1 [5174, 5326] * | TAIR10 CDS <NA> 0
## 16 Chr1 [5439, 5899] * | TAIR10 exon <NA> <NA>
## 17 Chr1 [5439, 5630] * | TAIR10 CDS <NA> 0
## 18 Chr1 [5631, 5899] * | TAIR10 three_prime_UTR <NA> <NA>
## ID Name Note Parent Index
## <character> <character> <CharacterList> <CharacterList> <character>
## 2 AT1G01010.1 AT1G01010.1 AT1G01010 1
## 3 AT1G01010.1 AT1G01010.1 AT1G01010 1
## 4 AT1G01010.1-Protein AT1G01010.1 <NA>
## 5 <NA> <NA> AT1G01010.1 <NA>
## 6 <NA> <NA> AT1G01010.1 <NA>
## ... ... ... ... ... ...
## 14 <NA> <NA> AT1G01010.1 <NA>
## 15 <NA> <NA> AT1G01010.1,AT1G01010.1-Protein <NA>
## 16 <NA> <NA> AT1G01010.1 <NA>
## 17 <NA> <NA> AT1G01010.1,AT1G01010.1-Protein <NA>
## 18 <NA> <NA> AT1G01010.1 <NA>
## Derives_from
## <character>
## 2 <NA>
## 3 <NA>
## 4 AT1G01010.1
## 5 <NA>
## 6 <NA>
## ... ...
## 14 <NA>
## 15 <NA>
## 16 <NA>
## 17 <NA>
## 18 <NA>
## -------
## seqinfo: 7 sequences from an unspecified genome
GRangesList Objects
sp <- split(gff, seq(along=gff)) # Stores every range in separate component of a GRangesList object
split(gff, seqnames(gff)) # Stores ranges of each chromosome in separate component.
## GRangesList object of length 7:
## $Chr1
## GRanges object with 71 ranges and 10 metadata columns:
## seqnames ranges strand | source type score phase
## <Rle> <IRanges> <Rle> | <factor> <factor> <numeric> <integer>
## 2 Chr1 [3631, 5899] * | TAIR10 mRNA <NA> <NA>
## 3 Chr1 [3631, 5899] * | TAIR10 mRNA <NA> <NA>
## 4 Chr1 [3760, 5630] * | TAIR10 protein <NA> <NA>
## 5 Chr1 [3631, 3913] * | TAIR10 exon <NA> <NA>
## 6 Chr1 [3631, 3759] * | TAIR10 five_prime_UTR <NA> <NA>
## ... ... ... ... ... ... ... ... ...
## 68 Chr1 [13335, 13714] * | TAIR10 exon <NA> <NA>
## 69 Chr1 [12941, 13173] * | TAIR10 five_prime_UTR <NA> <NA>
## 70 Chr1 [11864, 12940] * | TAIR10 CDS <NA> 0
## 71 Chr1 [11649, 11863] * | TAIR10 three_prime_UTR <NA> <NA>
## 72 Chr1 [11649, 13173] * | TAIR10 exon <NA> <NA>
## ID Name Note Parent Index
## <character> <character> <CharacterList> <CharacterList> <character>
## 2 AT1G01010.1 AT1G01010.1 AT1G01010 1
## 3 AT1G01010.1 AT1G01010.1 AT1G01010 1
## 4 AT1G01010.1-Protein AT1G01010.1 <NA>
## 5 <NA> <NA> AT1G01010.1 <NA>
## 6 <NA> <NA> AT1G01010.1 <NA>
## ... ... ... ... ... ...
## 68 <NA> <NA> AT1G01030.1 <NA>
## 69 <NA> <NA> AT1G01030.1 <NA>
## 70 <NA> <NA> AT1G01030.1,AT1G01030.1-Protein <NA>
## 71 <NA> <NA> AT1G01030.1 <NA>
## 72 <NA> <NA> AT1G01030.1 <NA>
## Derives_from
## <character>
## 2 <NA>
## 3 <NA>
## 4 AT1G01010.1
## 5 <NA>
## 6 <NA>
## ... ...
## 68 <NA>
## 69 <NA>
## 70 <NA>
## 71 <NA>
## 72 <NA>
##
## ...
## <6 more elements>
## -------
## seqinfo: 7 sequences from an unspecified genome
unlist(sp) # Returns data as GRanges object
## GRanges object with 442 ranges and 10 metadata columns:
## seqnames ranges strand | source type score phase
## <Rle> <IRanges> <Rle> | <factor> <factor> <numeric> <integer>
## 1.2 Chr1 [3631, 5899] * | TAIR10 mRNA <NA> <NA>
## 2.3 Chr1 [3631, 5899] * | TAIR10 mRNA <NA> <NA>
## 3.4 Chr1 [3760, 5630] * | TAIR10 protein <NA> <NA>
## 4.5 Chr1 [3631, 3913] * | TAIR10 exon <NA> <NA>
## 5.6 Chr1 [3631, 3759] * | TAIR10 five_prime_UTR <NA> <NA>
## ... ... ... ... ... ... ... ... ...
## 438.445 ChrM [11918, 12241] * | TAIR10 gene <NA> <NA>
## 439.446 ChrM [11918, 12241] * | TAIR10 mRNA <NA> <NA>
## 440.447 ChrM [11918, 12241] * | TAIR10 protein <NA> <NA>
## 441.448 ChrM [11918, 12241] * | TAIR10 exon <NA> <NA>
## 442.449 ChrM [11918, 12241] * | TAIR10 CDS <NA> 0
## ID Name Note Parent
## <character> <character> <CharacterList> <CharacterList>
## 1.2 AT1G01010.1 AT1G01010.1 AT1G01010
## 2.3 AT1G01010.1 AT1G01010.1 AT1G01010
## 3.4 AT1G01010.1-Protein AT1G01010.1
## 4.5 <NA> <NA> AT1G01010.1
## 5.6 <NA> <NA> AT1G01010.1
## ... ... ... ... ...
## 438.445 ATMG00030 ATMG00030 protein_coding_gene
## 439.446 ATMG00030.1 ATMG00030.1 ATMG00030
## 440.447 ATMG00030.1-Protein ATMG00030.1
## 441.448 <NA> <NA> ATMG00030.1
## 442.449 <NA> <NA> ATMG00030.1,ATMG00030.1-Protein
## Index Derives_from
## <character> <character>
## 1.2 1 <NA>
## 2.3 1 <NA>
## 3.4 <NA> AT1G01010.1
## 4.5 <NA> <NA>
## 5.6 <NA> <NA>
## ... ... ...
## 438.445 <NA> <NA>
## 439.446 1 <NA>
## 440.447 <NA> ATMG00030.1
## 441.448 <NA> <NA>
## 442.449 <NA> <NA>
## -------
## seqinfo: 7 sequences from an unspecified genome
sp[1:4, "type"] # Subsetting of GRangesList objects is similar to GRanges objects.
## GRangesList object of length 4:
## $1
## GRanges object with 1 range and 1 metadata column:
## seqnames ranges strand | type
## <Rle> <IRanges> <Rle> | <factor>
## 2 Chr1 [3631, 5899] * | mRNA
##
## $2
## GRanges object with 1 range and 1 metadata column:
## seqnames ranges strand | type
## 3 Chr1 [3631, 5899] * | mRNA
##
## $3
## GRanges object with 1 range and 1 metadata column:
## seqnames ranges strand | type
## 4 Chr1 [3760, 5630] * | protein
##
## ...
## <1 more element>
## -------
## seqinfo: 7 sequences from an unspecified genome
lapply(sp[1:4], length) # Looping over GRangesList objects similar to lists
## $`1`
## [1] 1
##
## $`2`
## [1] 1
##
## $`3`
## [1] 1
##
## $`4`
## [1] 1