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 = TRUEandchar = 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