add_target_counts.Rd
Count spacer matches among targets
add_target_counts( spacers, targets, bsgenome, mismatches = 2, pam = "NGG", outdir = OUTDIR, verbose = TRUE )
spacers | spacer |
---|---|
targets | target |
bsgenome | |
mismatches | number (default 2): max number of mismatches to consider |
pam | string (default 'NGG') pam pattern to expand |
outdir | dir where output is written to |
verbose | TRUE (default) or FALSE |
updated spacer GRanges-class
Expands iupac amgiguities in the pam sequence. Matches all resulting sequences against (indexes) target and genome. Adds match counts to GRanges object, and then returns it.
# TFBS example #------------- bsgenome <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10 bedfile <- system.file('extdata/SRF.bed', package = 'multicrispr') targets <- extend(bed_to_granges(bedfile, genome = 'mm10'))#>#>#>add_target_counts(spacers, targets, bsgenome)#>#>#>#>#>#>#>#>#>#>#>#>#> GRanges object with 10159 ranges and 11 metadata columns: #> seqnames ranges strand | targetname targetstart #> <Rle> <IRanges> <Rle> | <character> <integer> #> T0001_r_5 chr1 4712619-4712638 - | T0001 4712628 #> T0001_r_4 chr1 4712620-4712639 - | T0001 4712628 #> T0001_r_3 chr1 4712627-4712646 - | T0001 4712628 #> T0001_r_2 chr1 4712633-4712652 - | T0001 4712628 #> T0001_r_1 chr1 4712634-4712653 - | T0001 4712628 #> ... ... ... ... . ... ... #> T1974_r_3 chrY 89126492-89126511 - | T1974 89126494 #> T1974_f_3 chrY 89126496-89126515 + | T1974 89126494 #> T1974_r_2 chrY 89126499-89126518 - | T1974 89126494 #> T1974_r_1 chrY 89126500-89126519 - | T1974 89126494 #> T1974_f_4 chrY 89126501-89126520 + | T1974 89126494 #> targetend crisprname crisprspacer crisprpam name #> <integer> <character> <character> <character> <character> #> T0001_r_5 4712643 T0001_r_5 ATATAAGGGCATTGGAAGAA GGG SRF_MA0083.3 #> T0001_r_4 4712643 T0001_r_4 AATATAAGGGCATTGGAAGA AGG SRF_MA0083.3 #> T0001_r_3 4712643 T0001_r_3 TGGAGACAATATAAGGGCAT TGG SRF_MA0083.3 #> T0001_r_2 4712643 T0001_r_2 TTCTGCTGGAGACAATATAA GGG SRF_MA0083.3 #> T0001_r_1 4712643 T0001_r_1 CTTCTGCTGGAGACAATATA AGG SRF_MA0083.3 #> ... ... ... ... ... ... #> T1974_r_3 89126509 T1974_r_3 TTTGCCCATACTAGGGAGAG CGG SRF_MA0083.3 #> T1974_f_3 89126509 T1974_f_3 CCCTAGTATGGGCAAATATA TGG SRF_MA0083.3 #> T1974_r_2 89126509 T1974_r_2 CCATATATTTGCCCATACTA GGG SRF_MA0083.3 #> T1974_r_1 89126509 T1974_r_1 TCCATATATTTGCCCATACT AGG SRF_MA0083.3 #> T1974_f_4 89126509 T1974_f_4 GTATGGGCAAATATATGGAA TGG SRF_MA0083.3 #> score T0 T1 T2 #> <numeric> <integer> <integer> <integer> #> T0001_r_5 10.49542 1 973 97 #> T0001_r_4 10.49542 1 960 105 #> T0001_r_3 10.49542 1 975 95 #> T0001_r_2 10.49542 2 827 237 #> T0001_r_1 10.49542 825 242 19 #> ... ... ... ... ... #> T1974_r_3 4.54393 5 3 7 #> T1974_f_3 4.54393 5 1 9 #> T1974_r_2 4.54393 5 1 9 #> T1974_r_1 4.54393 6 0 9 #> T1974_f_4 4.54393 6 0 9 #> ------- #> seqinfo: 66 sequences (1 circular) from mm10 genome