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Parse alternative splicing event identifier

Usage

parseSplicingEvent(
  event,
  char = FALSE,
  pretty = FALSE,
  extra = NULL,
  coords = FALSE,
  data = NULL
)

Arguments

event

Character: event identifier

char

Boolean: return character vector instead of list with parsed values?

pretty

Boolean: return a prettier name of the event identifier?

extra

Character: extra information to add (such as species and assembly version); only used if pretty = TRUE and char = TRUE

coords

Boolean: display extra coordinates regarding the alternative and constitutive regions of alternative splicing events? Only used if char = FALSE

data

Matrix or data frame: alternative splicing information

Value

Data.frame containing type of event, chromosome, strand, gene and position of alternative splicing events or character with that same information (depending on what is available)

Examples

events <- c(
  "A3SS_15_+_63353138_63353912_63353397_TPM1",
  "A3SS_11_-_61118463_61117115_61117894_CYB561A3",
  "A5SS_21_+_48055675_48056459_48056808_PRMT2",
  "A5SS_1_-_1274742_1274667_1274033_DVL1",
  "AFE_9_+_131902430_131901928_131904724_PPP2R4",
  "AFE_5_-_134686513_134688636_134681747_H2AFY",
  "ALE_12_+_56554104_56554410_56555171_MYL6",
  "ALE_8_-_38314874_38287466_38285953_FGFR1",
  "SE_9_+_6486925_6492303_6492401_6493826_UHRF2",
  "SE_19_-_5218431_5216778_5216731_5215606_PTPRS",
  "MXE_15_+_63335142_63335905_63336030_63336226_63336351_63349184_TPM1",
  "MXE_17_-_74090495_74087316_74087224_74086478_74086410_74085401_EXOC7")
parseSplicingEvent(events)
#>                                                                      type chrom
#> A3SS_15_+_63353138_63353912_63353397_TPM1                            A3SS    15
#> A3SS_11_-_61118463_61117115_61117894_CYB561A3                        A3SS    11
#> A5SS_21_+_48055675_48056459_48056808_PRMT2                           A5SS    21
#> A5SS_1_-_1274742_1274667_1274033_DVL1                                A5SS     1
#> AFE_9_+_131902430_131901928_131904724_PPP2R4                          AFE     9
#> AFE_5_-_134686513_134688636_134681747_H2AFY                           AFE     5
#> ALE_12_+_56554104_56554410_56555171_MYL6                              ALE    12
#> ALE_8_-_38314874_38287466_38285953_FGFR1                              ALE     8
#> SE_9_+_6486925_6492303_6492401_6493826_UHRF2                           SE     9
#> SE_19_-_5218431_5216778_5216731_5215606_PTPRS                          SE    19
#> MXE_15_+_63335142_63335905_63336030_63336226_63336351_63349184_TPM1   MXE    15
#> MXE_17_-_74090495_74087316_74087224_74086478_74086410_74085401_EXOC7  MXE    17
#>                                                                      strand
#> A3SS_15_+_63353138_63353912_63353397_TPM1                                 +
#> A3SS_11_-_61118463_61117115_61117894_CYB561A3                             -
#> A5SS_21_+_48055675_48056459_48056808_PRMT2                                +
#> A5SS_1_-_1274742_1274667_1274033_DVL1                                     -
#> AFE_9_+_131902430_131901928_131904724_PPP2R4                              +
#> AFE_5_-_134686513_134688636_134681747_H2AFY                               -
#> ALE_12_+_56554104_56554410_56555171_MYL6                                  +
#> ALE_8_-_38314874_38287466_38285953_FGFR1                                  -
#> SE_9_+_6486925_6492303_6492401_6493826_UHRF2                              +
#> SE_19_-_5218431_5216778_5216731_5215606_PTPRS                             -
#> MXE_15_+_63335142_63335905_63336030_63336226_63336351_63349184_TPM1       +
#> MXE_17_-_74090495_74087316_74087224_74086478_74086410_74085401_EXOC7      -
#>                                                                          gene
#> A3SS_15_+_63353138_63353912_63353397_TPM1                                TPM1
#> A3SS_11_-_61118463_61117115_61117894_CYB561A3                        CYB561A3
#> A5SS_21_+_48055675_48056459_48056808_PRMT2                              PRMT2
#> A5SS_1_-_1274742_1274667_1274033_DVL1                                    DVL1
#> AFE_9_+_131902430_131901928_131904724_PPP2R4                           PPP2R4
#> AFE_5_-_134686513_134688636_134681747_H2AFY                             H2AFY
#> ALE_12_+_56554104_56554410_56555171_MYL6                                 MYL6
#> ALE_8_-_38314874_38287466_38285953_FGFR1                                FGFR1
#> SE_9_+_6486925_6492303_6492401_6493826_UHRF2                            UHRF2
#> SE_19_-_5218431_5216778_5216731_5215606_PTPRS                           PTPRS
#> MXE_15_+_63335142_63335905_63336030_63336226_63336351_63349184_TPM1      TPM1
#> MXE_17_-_74090495_74087316_74087224_74086478_74086410_74085401_EXOC7    EXOC7
#>                                                                               pos
#> A3SS_15_+_63353138_63353912_63353397_TPM1                            63353138....
#> A3SS_11_-_61118463_61117115_61117894_CYB561A3                        61117115....
#> A5SS_21_+_48055675_48056459_48056808_PRMT2                           48055675....
#> A5SS_1_-_1274742_1274667_1274033_DVL1                                1274033,....
#> AFE_9_+_131902430_131901928_131904724_PPP2R4                         13190192....
#> AFE_5_-_134686513_134688636_134681747_H2AFY                          13468174....
#> ALE_12_+_56554104_56554410_56555171_MYL6                             56554104....
#> ALE_8_-_38314874_38287466_38285953_FGFR1                             38285953....
#> SE_9_+_6486925_6492303_6492401_6493826_UHRF2                         6486925,....
#> SE_19_-_5218431_5216778_5216731_5215606_PTPRS                        5215606,....
#> MXE_15_+_63335142_63335905_63336030_63336226_63336351_63349184_TPM1  63335142....
#> MXE_17_-_74090495_74087316_74087224_74086478_74086410_74085401_EXOC7 74085401....
#>                                                                          start
#> A3SS_15_+_63353138_63353912_63353397_TPM1                             63353138
#> A3SS_11_-_61118463_61117115_61117894_CYB561A3                         61117115
#> A5SS_21_+_48055675_48056459_48056808_PRMT2                            48055675
#> A5SS_1_-_1274742_1274667_1274033_DVL1                                  1274033
#> AFE_9_+_131902430_131901928_131904724_PPP2R4                         131901928
#> AFE_5_-_134686513_134688636_134681747_H2AFY                          134681747
#> ALE_12_+_56554104_56554410_56555171_MYL6                              56554104
#> ALE_8_-_38314874_38287466_38285953_FGFR1                              38285953
#> SE_9_+_6486925_6492303_6492401_6493826_UHRF2                           6486925
#> SE_19_-_5218431_5216778_5216731_5215606_PTPRS                          5215606
#> MXE_15_+_63335142_63335905_63336030_63336226_63336351_63349184_TPM1   63335142
#> MXE_17_-_74090495_74087316_74087224_74086478_74086410_74085401_EXOC7  74085401
#>                                                                            end
#> A3SS_15_+_63353138_63353912_63353397_TPM1                             63353912
#> A3SS_11_-_61118463_61117115_61117894_CYB561A3                         61118463
#> A5SS_21_+_48055675_48056459_48056808_PRMT2                            48056808
#> A5SS_1_-_1274742_1274667_1274033_DVL1                                  1274742
#> AFE_9_+_131902430_131901928_131904724_PPP2R4                         131904724
#> AFE_5_-_134686513_134688636_134681747_H2AFY                          134688636
#> ALE_12_+_56554104_56554410_56555171_MYL6                              56555171
#> ALE_8_-_38314874_38287466_38285953_FGFR1                              38314874
#> SE_9_+_6486925_6492303_6492401_6493826_UHRF2                           6493826
#> SE_19_-_5218431_5216778_5216731_5215606_PTPRS                          5218431
#> MXE_15_+_63335142_63335905_63336030_63336226_63336351_63349184_TPM1   63349184
#> MXE_17_-_74090495_74087316_74087224_74086478_74086410_74085401_EXOC7  74090495
#>                                                                      subtype
#> A3SS_15_+_63353138_63353912_63353397_TPM1                               A3SS
#> A3SS_11_-_61118463_61117115_61117894_CYB561A3                           A3SS
#> A5SS_21_+_48055675_48056459_48056808_PRMT2                              A5SS
#> A5SS_1_-_1274742_1274667_1274033_DVL1                                   A5SS
#> AFE_9_+_131902430_131901928_131904724_PPP2R4                             AFE
#> AFE_5_-_134686513_134688636_134681747_H2AFY                              AFE
#> ALE_12_+_56554104_56554410_56555171_MYL6                                 ALE
#> ALE_8_-_38314874_38287466_38285953_FGFR1                                 ALE
#> SE_9_+_6486925_6492303_6492401_6493826_UHRF2                              SE
#> SE_19_-_5218431_5216778_5216731_5215606_PTPRS                             SE
#> MXE_15_+_63335142_63335905_63336030_63336226_63336351_63349184_TPM1      MXE
#> MXE_17_-_74090495_74087316_74087224_74086478_74086410_74085401_EXOC7     MXE