Find crispr spacers in targetranges

find_spacers(
  gr,
  bsgenome,
  spacer = strrep("N", 20),
  pam = "NGG",
  complement = TRUE,
  ontargetmethod = c("Doench2014", "Doench2016")[1],
  offtargetmethod = c("bowtie", "pdict")[1],
  offtargetfilterby = character(0),
  subtract_targets = FALSE,
  mismatches = 2,
  indexedgenomesdir = INDEXEDGENOMESDIR,
  outdir = OUTDIR,
  verbose = TRUE,
  plot = TRUE,
  ...
)

Arguments

gr	`GRanges-class`
bsgenome	`BSgenome-class`
spacer	string: spacer pattern in extended IUPAC alphabet
pam	string: pam pattern in extended IUPAC alphabet
complement	TRUE (default) or FALSE: also search in compl ranges?
ontargetmethod	'Doench2016' or 'Doench2016': on-target scoring method
offtargetmethod	'bowtie' (default) or 'pdict'
offtargetfilterby	filter for best off-target counts by this variable
subtract_targets	TRUE or FALSE (default): whether to subtract target (mis)matches from offtarget counts
mismatches	0-3: allowed mismatches in offtargetanalysis (choose mismatch=-1 to suppress offtarget analysis)
indexedgenomesdir	directory with Bowtie-indexed genomes (as produced with `index_genome`)
outdir	directory where bowtie analysis results are written to
verbose	TRUE (default) or FALSE
plot	TRUE (default) or FALSE
...	passed to plot_intervals

Value

GRanges-class

Examples

# PE example
#-----------
    require(magrittr)
    bsgenome <- BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38
    gr <- char_to_granges(c(PRNP = 'chr20:4699600:+',             # snp
                            HBB  = 'chr11:5227002:-',             # snp
                            HEXA = 'chr15:72346580-72346583:-',   # del
                            CFTR = 'chr7:117559593-117559595:+'), # ins
                          bsgenome)
    plot_intervals(gr)
    find_primespacers(gr, bsgenome)
#> Find primespacers for 4 targets
#> 	Found 10 primespacers
#> 	Count offtargets with max 0 mismatches using bowtie
#> 		Count genome (mis)matches
#> 			Expand iupac ambiguities in pam
#> 			Write reads to ~/multicrisprout/spacers.fa
#> 			Map reads: ~/multicrisprout/spacers/spacers_to_BSgenome.Hsapiens.UCSC.hg38.txt
#> 			Load results
#> 				Read 53 hits with max 1 mismatch(es)
#> 				Retain 20 after removing NGG 'N' mismatches (avoid double counting expanded pams)
#> 				Retain 20 after removing NGG 'G1' mismatches(except for NGG -> NAG, which is allowed)
#> 				Retain 20 after removing NGG 'G2' mismatches
#> 				Retain 11 after removing more than 0 mismatches
#> 			Count matches
#> 		Count off-targets
#> 		       9 are off0 free
#> 	Score ontargets
#> 		Add (4-23-3) contextseqs
#> 		Score contextseqs with Doench2014
#> Find nickspacers
#> Find spacers in 10 targets
#> 	Found 32 spacers
#> 	Count offtargets with max 2 mismatches using bowtie
#> 		Count genome (mis)matches
#> 			Expand iupac ambiguities in pam
#> 			Write reads to ~/multicrisprout/spacers.fa
#> 			Map reads: ~/multicrisprout/spacers/spacers_to_BSgenome.Hsapiens.UCSC.hg38.txt
#> 			Load results
#> 				Read 91 hits with max 2 mismatch(es)
#> 				Retain 37 after removing NGG 'N' mismatches (avoid double counting expanded pams)
#> 				Retain 36 after removing NGG 'G1' mismatches(except for NGG -> NAG, which is allowed)
#> 				Retain 33 after removing NGG 'G2' mismatches
#> 				Retain 33 after removing more than 2 mismatches
#> 			Count matches
#> 		Count off-targets
#> 		       30 are off0 free
#> 		       32 are off1 free
#> 		       24 are off2 free
#> 	Filter for best offtarget counts
#> 		Retain 32 with best off0 counts per pename
#> 		Retain 32 with best off1 counts per pename
#> 		Retain 24 with best off2 counts per pename
#> 	Score ontargets
#> 		Add (4-23-3) contextseqs
#> 		Score contextseqs with Doench2014
#> Warning: Removed 34 rows containing missing values (geom_point).
#> Warning: Removed 34 rows containing missing values (geom_point).
#> GRanges object with 10 ranges and 21 metadata columns:
#>          seqnames              ranges strand |  targetname targetstart
#>             <Rle>           <IRanges>  <Rle> | <character>   <integer>
#>   CFTR_1     chr7 117559575-117559594      + |        CFTR   117559593
#>   CFTR_2     chr7 117559606-117559625      - |        CFTR   117559593
#>    HBB_1    chr11     5227003-5227022      - |         HBB     5227002
#>    HBB_2    chr11     5226984-5227003      + |         HBB     5227002
#>   HEXA_1    chr15   72346551-72346570      + |        HEXA    72346580
#>   HEXA_2    chr15   72346558-72346577      + |        HEXA    72346580
#>   PRNP_1    chr20     4699568-4699587      + |        PRNP     4699600
#>   PRNP_2    chr20     4699569-4699588      + |        PRNP     4699600
#>   PRNP_3    chr20     4699575-4699594      + |        PRNP     4699600
#>   PRNP_4    chr20     4699578-4699597      + |        PRNP     4699600
#>          targetend  crisprname         crisprspacer   crisprpam  crisprprimer
#>          <integer> <character>          <character> <character>   <character>
#>   CFTR_1 117559595      CFTR_1 ATTAAAGAAAATATCATCTT         TGG AAGAAAATATCAT
#>   CFTR_2 117559595      CFTR_2 TCTGTATCTATATTCATCAT         AGG TATCTATATTCAT
#>    HBB_1   5227002       HBB_1 CATGGTGCATCTGACTCCTG         AGG GTGCATCTGACTC
#>    HBB_2   5227002       HBB_2 GTAACGGCAGACTTCTCCTC         AGG CGGCAGACTTCTC
#>   HEXA_1  72346583      HEXA_1 TGTAGAAATCCTTCCAGTCA         GGG GAAATCCTTCCAG
#>   HEXA_2  72346583      HEXA_2 ATCCTTCCAGTCAGGGCCAT         AGG TTCCAGTCAGGGC
#>   PRNP_1   4699600      PRNP_1 AGCAGCTGGGGCAGTGGTGG         GGG GCTGGGGCAGTGG
#>   PRNP_2   4699600      PRNP_2 GCAGCTGGGGCAGTGGTGGG         GGG CTGGGGCAGTGGT
#>   PRNP_3   4699600      PRNP_3 GGGGCAGTGGTGGGGGGCCT         TGG CAGTGGTGGGGGG
#>   PRNP_4   4699600      PRNP_4 GCAGTGGTGGGGGGCCTTGG         CGG TGGTGGGGGGCCT
#>          crisprtranscript               crisprextension
#>               <character>                   <character>
#>   CFTR_1 CTTTGGTGTTTCCTAT ATAGGAAACACCAAAGATGATATTTTCTT
#>   CFTR_2 CATAGGAAACACCAAA TTTGGTGTTTCCTATGATGAATATAGATA
#>    HBB_1 CTGAGGAGAAGTCTGC GCAGACTTCTCCTCAGGAGTCAGATGCAC
#>    HBB_2 CTCAGGAGTCAGATGC GCATCTGACTCCTGAGGAGAAGTCTGCCG
#>   HEXA_1 TCAGGGCCATAGGATA TATCCTATGGCCCTGACTGGAAGGATTTC
#>   HEXA_2 CATAGGATATACGGTT AACCGTATATCCTATGGCCCTGACTGGAA
#>   PRNP_1 TGGGGGGCCTTGGCGG CCGCCAAGGCCCCCCACCACTGCCCCAGC
#>   PRNP_2 GGGGGGCCTTGGCGGC GCCGCCAAGGCCCCCCACCACTGCCCCAG
#>   PRNP_3 CCTTGGCGGCTACATG CATGTAGCCGCCAAGGCCCCCCACCACTG
#>   PRNP_4 TGGCGGCTACATGCTG CAGCATGTAGCCGCCAAGGCCCCCCACCA
#>                      crisprextrange       off      off0 Doench2014
#>                         <character> <numeric> <numeric>  <numeric>
#>   CFTR_1 chr7:117559579-117559607:-         0         0 0.03399990
#>   CFTR_2 chr7:117559593-117559621:+         0         0 0.22337056
#>    HBB_1    chr11:5226990-5227018:+         1         1 0.13111422
#>    HBB_2    chr11:5226988-5227016:-         0         0 0.41398065
#>   HEXA_1  chr15:72346555-72346583:-         0         0 0.10728361
#>   HEXA_2  chr15:72346562-72346590:-         0         0 0.03942528
#>   PRNP_1    chr20:4699572-4699600:-         0         0 0.00994899
#>   PRNP_2    chr20:4699573-4699601:-         0         0 0.04496627
#>   PRNP_3    chr20:4699579-4699607:-         0         0 0.00996254
#>   PRNP_4    chr20:4699582-4699610:-         0         0 0.20935863
#>                                                                                                        nickrange
#>                                                                                                      <character>
#>   CFTR_1                                                                              chr7:117559646-117559665:-
#>   CFTR_2                                                                              chr7:117559506-117559525:+
#>    HBB_1                                                         chr11:5226916-5226935:+;chr11:5226917-5226936:+
#>    HBB_2                                                                                                    <NA>
#>   HEXA_1 chr15:72346621-72346640:-;chr15:72346628-72346647:-;chr15:72346632-72346651:-;chr15:72346647-72346666:-
#>   HEXA_2 chr15:72346621-72346640:-;chr15:72346628-72346647:-;chr15:72346632-72346651:-;chr15:72346647-72346666:-
#>   PRNP_1                                 chr20:4699632-4699651:-;chr20:4699633-4699652:-;chr20:4699664-4699683:-
#>   PRNP_2                                 chr20:4699632-4699651:-;chr20:4699633-4699652:-;chr20:4699664-4699683:-
#>   PRNP_3                                 chr20:4699632-4699651:-;chr20:4699633-4699652:-;chr20:4699664-4699683:-
#>   PRNP_4                                 chr20:4699632-4699651:-;chr20:4699633-4699652:-;chr20:4699664-4699683:-
#>                                                                                   nickspacer
#>                                                                                  <character>
#>   CFTR_1                                                                AGTTTCTTACCTCTTCTAGT
#>   CFTR_2                                                                GAGGGTAAAATTAAGCACAG
#>    HBB_1                                           ACCTTGATACCAACCTGCCC;CCTTGATACCAACCTGCCCA
#>    HBB_2                                                                                <NA>
#>   HEXA_1 TGGTCACCAAGGCCGGCTTC;CTGGAACTGGTCACCAAGGC;GGAGCTGGAACTGGTCACCA;AGTGAACTATATGAAGGAGC
#>   HEXA_2 TGGTCACCAAGGCCGGCTTC;CTGGAACTGGTCACCAAGGC;GGAGCTGGAACTGGTCACCA;AGTGAACTATATGAAGGAGC
#>   PRNP_1                      TCACTGCCGAAATGTATGAT;GTCACTGCCGAAATGTATGA;GCATGTTTTCACGATAGTAA
#>   PRNP_2                      TCACTGCCGAAATGTATGAT;GTCACTGCCGAAATGTATGA;GCATGTTTTCACGATAGTAA
#>   PRNP_3                      TCACTGCCGAAATGTATGAT;GTCACTGCCGAAATGTATGA;GCATGTTTTCACGATAGTAA
#>   PRNP_4                      TCACTGCCGAAATGTATGAT;GTCACTGCCGAAATGTATGA;GCATGTTTTCACGATAGTAA
#>                  nickpam     nickoff    nickoff0    nickoff1    nickoff2
#>              <character> <character> <character> <character> <character>
#>   CFTR_1             TGG           0           0           0           0
#>   CFTR_2             TGG           0           0           0           0
#>    HBB_1         AGG;GGG         1;1         1;1         0;0         0;0
#>    HBB_2            <NA>        <NA>        <NA>        <NA>        <NA>
#>   HEXA_1 CGG;CGG;AGG;TGG     0;0;0;0     0;0;0;0     0;0;0;0     0;0;0;0
#>   HEXA_2 CGG;CGG;AGG;TGG     0;0;0;0     0;0;0;0     0;0;0;0     0;0;0;0
#>   PRNP_1     GGG;TGG;CGG       0;0;0       0;0;0       0;0;0       0;0;0
#>   PRNP_2     GGG;TGG;CGG       0;0;0       0;0;0       0;0;0       0;0;0
#>   PRNP_3     GGG;TGG;CGG       0;0;0       0;0;0       0;0;0       0;0;0
#>   PRNP_4     GGG;TGG;CGG       0;0;0       0;0;0       0;0;0       0;0;0
#>              nickDoench2014
#>                 <character>
#>   CFTR_1               0.38
#>   CFTR_2               0.49
#>    HBB_1          0.06;0.42
#>    HBB_2               <NA>
#>   HEXA_1 0.01;0.05;0.32;0.2
#>   HEXA_2 0.01;0.05;0.32;0.2
#>   PRNP_1     0.14;0.32;0.52
#>   PRNP_2     0.14;0.32;0.52
#>   PRNP_3     0.14;0.32;0.52
#>   PRNP_4     0.14;0.32;0.52
#>   -------
#>   seqinfo: 595 sequences (1 circular) from hg38 genome
    find_spacers(extend_for_pe(gr), bsgenome, complement=FALSE, mismatches=0)
#> Find spacers in 8 targets
#> 	Found 10 spacers
#> 	Count offtargets with max 0 mismatches using bowtie
#> 		Count genome (mis)matches
#> 			Expand iupac ambiguities in pam
#> 			Write reads to ~/multicrisprout/spacers.fa
#> 			Map reads: ~/multicrisprout/spacers/spacers_to_BSgenome.Hsapiens.UCSC.hg38.txt
#> 			Load results
#> 				Read 53 hits with max 1 mismatch(es)
#> 				Retain 20 after removing NGG 'N' mismatches (avoid double counting expanded pams)
#> 				Retain 20 after removing NGG 'G1' mismatches(except for NGG -> NAG, which is allowed)
#> 				Retain 20 after removing NGG 'G2' mismatches
#> 				Retain 11 after removing more than 0 mismatches
#> 			Count matches
#> 		Count off-targets
#> 		       9 are off0 free
#> 	Score ontargets
#> 		Add (4-23-3) contextseqs
#> 		Score contextseqs with Doench2014
#> GRanges object with 10 ranges and 9 metadata columns:
#>            seqnames              ranges strand |  targetname targetstart
#>               <Rle>           <IRanges>  <Rle> | <character>   <integer>
#>     CFTR_f     chr7 117559575-117559594      + |        CFTR   117559593
#>     CFTR_r     chr7 117559606-117559625      - |        CFTR   117559593
#>      HBB_f    chr11     5226984-5227003      + |         HBB     5227002
#>      HBB_r    chr11     5227003-5227022      - |         HBB     5227002
#>   HEXA_f_1    chr15   72346551-72346570      + |        HEXA    72346580
#>   HEXA_f_2    chr15   72346558-72346577      + |        HEXA    72346580
#>   PRNP_f_1    chr20     4699568-4699587      + |        PRNP     4699600
#>   PRNP_f_2    chr20     4699569-4699588      + |        PRNP     4699600
#>   PRNP_f_3    chr20     4699575-4699594      + |        PRNP     4699600
#>   PRNP_f_4    chr20     4699578-4699597      + |        PRNP     4699600
#>            targetend  crisprname         crisprspacer   crisprpam       off
#>            <integer> <character>          <character> <character> <numeric>
#>     CFTR_f 117559595      CFTR_f ATTAAAGAAAATATCATCTT         TGG         0
#>     CFTR_r 117559595      CFTR_r TCTGTATCTATATTCATCAT         AGG         0
#>      HBB_f   5227002       HBB_f GTAACGGCAGACTTCTCCTC         AGG         0
#>      HBB_r   5227002       HBB_r CATGGTGCATCTGACTCCTG         AGG         1
#>   HEXA_f_1  72346583    HEXA_f_1 TGTAGAAATCCTTCCAGTCA         GGG         0
#>   HEXA_f_2  72346583    HEXA_f_2 ATCCTTCCAGTCAGGGCCAT         AGG         0
#>   PRNP_f_1   4699600    PRNP_f_1 AGCAGCTGGGGCAGTGGTGG         GGG         0
#>   PRNP_f_2   4699600    PRNP_f_2 GCAGCTGGGGCAGTGGTGGG         GGG         0
#>   PRNP_f_3   4699600    PRNP_f_3 GGGGCAGTGGTGGGGGGCCT         TGG         0
#>   PRNP_f_4   4699600    PRNP_f_4 GCAGTGGTGGGGGGCCTTGG         CGG         0
#>                 off0 Doench2014
#>            <numeric>  <numeric>
#>     CFTR_f         0 0.03399990
#>     CFTR_r         0 0.22337056
#>      HBB_f         0 0.41398065
#>      HBB_r         1 0.13111422
#>   HEXA_f_1         0 0.10728361
#>   HEXA_f_2         0 0.03942528
#>   PRNP_f_1         0 0.00994899
#>   PRNP_f_2         0 0.04496627
#>   PRNP_f_3         0 0.00996254
#>   PRNP_f_4         0 0.20935863
#>   -------
#>   seqinfo: 595 sequences (1 circular) from hg38 genome
          # complement = FALSE because extend_for_pe  already 
          # adds  reverse complements and does so in a strand-specific 
          # manner

# TFBS example
#-------------
    bsgenome <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10
    bedfile  <- system.file('extdata/SRF.bed', package='multicrispr')
    gr <- bed_to_granges(bedfile, 'mm10') %>% extend()
#> 	Read SRF.bed into GRanges
#> 		1974 ranges on 21 chromosomes
    gr %<>% extract(1:100)
    find_spacers(gr, bsgenome, subtract_targets = TRUE)
#> Find spacers in 100 targets
#> 	Retain 200 unique target ranges after adding inverse strands
#> 	Found 517 spacers
#> 	Count offtargets with max 2 mismatches using bowtie
#> 		Count genome (mis)matches
#> 			Expand iupac ambiguities in pam
#> 			Write reads to ~/multicrisprout/spacers.fa
#> 			Map reads: ~/multicrisprout/spacers/spacers_to_BSgenome.Mmusculus.UCSC.mm10.txt
#> 			Load results
#> 				Read 1033855 hits with max 2 mismatch(es)
#> 				Retain 357793 after removing NGG 'N' mismatches (avoid double counting expanded pams)
#> 				Retain 334703 after removing NGG 'G1' mismatches(except for NGG -> NAG, which is allowed)
#> 				Retain 313299 after removing NGG 'G2' mismatches
#> 				Retain 313299 after removing more than 2 mismatches
#> 			Count matches
#> 	Index target sequences
#> 		200 target ranges
#> 		200 ranges after merging overlaps
#> 		Write seqs  to ~/multicrisprout/targets.fa
#> 		Write index to ~/multicrisprout/targets
#> 		Count target cross-(mis)matches
#> 			Expand iupac ambiguities in pam
#> 			Write reads to ~/multicrisprout/spacers.fa
#> 			Map reads: ~/multicrisprout/spacers/spacers_to_targets.txt
#> 			Load results
#> 				Read 7451 hits with max 2 mismatch(es)
#> 				Retain 2177 after removing NGG 'N' mismatches (avoid double counting expanded pams)
#> 				Retain 2167 after removing NGG 'G1' mismatches(except for NGG -> NAG, which is allowed)
#> 				Retain 2010 after removing NGG 'G2' mismatches
#> 				Retain 2010 after removing more than 2 mismatches
#> 			Count matches
#> 		Count off-targets
#> 		       109 are off0 free
#> 		        94 are off1 free
#> 		        57 are off2 free
#> 	Score ontargets
#> 		Add (4-23-3) contextseqs
#> 		Score contextseqs with Doench2014
#> GRanges object with 517 ranges and 19 metadata columns:
#>                                  seqnames              ranges strand |
#>                                     <Rle>           <IRanges>  <Rle> |
#>       chr1:4712628-4712643:-_r_5     chr1     4712619-4712638      - |
#>       chr1:4712628-4712643:-_r_4     chr1     4712620-4712639      - |
#>       chr1:4712628-4712643:-_r_3     chr1     4712627-4712646      - |
#>       chr1:4712628-4712643:-_r_2     chr1     4712633-4712652      - |
#>       chr1:4712628-4712643:-_r_1     chr1     4712634-4712653      - |
#>                              ...      ...                 ...    ... .
#>     chr1:113368495-113368510:+_r     chr1 113368487-113368506      - |
#>   chr1:113368495-113368510:+_f_1     chr1 113368485-113368504      + |
#>   chr1:113368495-113368510:+_f_2     chr1 113368492-113368511      + |
#>   chr1:113368495-113368510:+_f_3     chr1 113368499-113368518      + |
#>   chr1:113368495-113368510:+_f_4     chr1 113368500-113368519      + |
#>                                                  targetname targetstart
#>                                                 <character>   <integer>
#>       chr1:4712628-4712643:-_r_5     chr1:4712628-4712643:-     4712628
#>       chr1:4712628-4712643:-_r_4     chr1:4712628-4712643:-     4712628
#>       chr1:4712628-4712643:-_r_3     chr1:4712628-4712643:-     4712628
#>       chr1:4712628-4712643:-_r_2     chr1:4712628-4712643:-     4712628
#>       chr1:4712628-4712643:-_r_1     chr1:4712628-4712643:-     4712628
#>                              ...                        ...         ...
#>     chr1:113368495-113368510:+_r chr1:113368495-113368510:+   113368495
#>   chr1:113368495-113368510:+_f_1 chr1:113368495-113368510:+   113368495
#>   chr1:113368495-113368510:+_f_2 chr1:113368495-113368510:+   113368495
#>   chr1:113368495-113368510:+_f_3 chr1:113368495-113368510:+   113368495
#>   chr1:113368495-113368510:+_f_4 chr1:113368495-113368510:+   113368495
#>                                  targetend                     crisprname
#>                                  <integer>                    <character>
#>       chr1:4712628-4712643:-_r_5   4712643     chr1:4712628-4712643:-_r_5
#>       chr1:4712628-4712643:-_r_4   4712643     chr1:4712628-4712643:-_r_4
#>       chr1:4712628-4712643:-_r_3   4712643     chr1:4712628-4712643:-_r_3
#>       chr1:4712628-4712643:-_r_2   4712643     chr1:4712628-4712643:-_r_2
#>       chr1:4712628-4712643:-_r_1   4712643     chr1:4712628-4712643:-_r_1
#>                              ...       ...                            ...
#>     chr1:113368495-113368510:+_r 113368510   chr1:113368495-113368510:+_r
#>   chr1:113368495-113368510:+_f_1 113368510 chr1:113368495-113368510:+_f_1
#>   chr1:113368495-113368510:+_f_2 113368510 chr1:113368495-113368510:+_f_2
#>   chr1:113368495-113368510:+_f_3 113368510 chr1:113368495-113368510:+_f_3
#>   chr1:113368495-113368510:+_f_4 113368510 chr1:113368495-113368510:+_f_4
#>                                          crisprspacer   crisprpam         name
#>                                           <character> <character>  <character>
#>       chr1:4712628-4712643:-_r_5 ATATAAGGGCATTGGAAGAA         GGG SRF_MA0083.3
#>       chr1:4712628-4712643:-_r_4 AATATAAGGGCATTGGAAGA         AGG SRF_MA0083.3
#>       chr1:4712628-4712643:-_r_3 TGGAGACAATATAAGGGCAT         TGG SRF_MA0083.3
#>       chr1:4712628-4712643:-_r_2 TTCTGCTGGAGACAATATAA         GGG SRF_MA0083.3
#>       chr1:4712628-4712643:-_r_1 CTTCTGCTGGAGACAATATA         AGG SRF_MA0083.3
#>                              ...                  ...         ...          ...
#>     chr1:113368495-113368510:+_r CTTATATTGTCTCCAGCAGA         AGG SRF_MA0083.3
#>   chr1:113368495-113368510:+_f_1 CTTCTGCTGGAGACAATATA         AGG SRF_MA0083.3
#>   chr1:113368495-113368510:+_f_2 TGGAGACAATATAAGGACAT         TGG SRF_MA0083.3
#>   chr1:113368495-113368510:+_f_3 AATATAAGGACATTGGAAGA         AGG SRF_MA0083.3
#>   chr1:113368495-113368510:+_f_4 ATATAAGGACATTGGAAGAA         GGG SRF_MA0083.3
#>                                      score        G0        G1        G2
#>                                  <numeric> <integer> <integer> <integer>
#>       chr1:4712628-4712643:-_r_5   10.4954         7      2473       356
#>       chr1:4712628-4712643:-_r_4   10.4954         7      2328       512
#>       chr1:4712628-4712643:-_r_3   10.4954         7      2358       392
#>       chr1:4712628-4712643:-_r_2   10.4954         8         4         5
#>       chr1:4712628-4712643:-_r_1   10.4954      1678      1083       198
#>                              ...       ...       ...       ...       ...
#>     chr1:113368495-113368510:+_r    9.7378      1652      1069       204
#>   chr1:113368495-113368510:+_f_1    9.7378      1678      1083       198
#>   chr1:113368495-113368510:+_f_2    9.7378      2353       393       199
#>   chr1:113368495-113368510:+_f_3    9.7378      2324       492       622
#>   chr1:113368495-113368510:+_f_4    9.7378      2468       350        97
#>                                         T0        T1        T2       off
#>                                  <integer> <integer> <integer> <integer>
#>       chr1:4712628-4712643:-_r_5         1        49         3      2783
#>       chr1:4712628-4712643:-_r_4         1        47         4      2795
#>       chr1:4712628-4712643:-_r_3         1        49         2      2705
#>       chr1:4712628-4712643:-_r_2         1         0         0        16
#>       chr1:4712628-4712643:-_r_1        44         9         2      2904
#>                              ...       ...       ...       ...       ...
#>     chr1:113368495-113368510:+_r        44         9         1      2871
#>   chr1:113368495-113368510:+_f_1        44         9         2      2904
#>   chr1:113368495-113368510:+_f_2        49         3         2      2891
#>   chr1:113368495-113368510:+_f_3        47         5         0      3386
#>   chr1:113368495-113368510:+_f_4        49         4         0      2862
#>                                       off0      off1      off2 Doench2014
#>                                  <integer> <integer> <integer>  <numeric>
#>       chr1:4712628-4712643:-_r_5         6      2424       353 0.16491179
#>       chr1:4712628-4712643:-_r_4         6      2281       508 0.00721485
#>       chr1:4712628-4712643:-_r_3         6      2309       390 0.12161212
#>       chr1:4712628-4712643:-_r_2         7         4         5 0.16315246
#>       chr1:4712628-4712643:-_r_1      1634      1074       196 0.07629138
#>                              ...       ...       ...       ...        ...
#>     chr1:113368495-113368510:+_r      1608      1060       203  0.0872713
#>   chr1:113368495-113368510:+_f_1      1634      1074       196  0.1412653
#>   chr1:113368495-113368510:+_f_2      2304       390       197  0.1200911
#>   chr1:113368495-113368510:+_f_3      2277       487       622  0.0139888
#>   chr1:113368495-113368510:+_f_4      2419       346        97  0.4236408
#>   -------
#>   seqinfo: 66 sequences (1 circular) from mm10 genome

Find crispr spacers in targetranges

Arguments

Value

See also

Examples