Filter transposable elements from rmsk reference based on given their gene, family, and class ID.
rmskFilter.RdFor filtering out the select transposable elements from gene, family, and class to down-stream analysis, we provide this function to help quickly list all options out. You can run this function first setting show to TRUE to see every possibility. Then you provide a character vector including the name of family/class you want to select. The function will then return a subset of the rmsk dataframe.
Arguments
- rmskInfo
rmsk dataframe, with three columns, gene_id, family_id, and class_id
- gene
a vector including the gene names you want
- family
a vector including the family names you want
- class
a vector including the class names you want
- show
if you want to first see all possible family/class, set this as TRUE
Examples
data(hg19rmsk_info)
df <- hg19rmsk_info
#list all possibilities
rmskFilter(df, show=TRUE)
#> [1] "Family ID"
#> [1] "========================="
#> [1] "Alu" "hAT-Charlie" "ERV1" "MIR"
#> [5] "L2" "ERVL" "TcMar-Tigger" "ERVL-MaLR"
#> [9] "L1" "Gypsy" "CR1" "TcMar-Mariner"
#> [13] "RNA" "hAT-Tip100" "DNA" "Deu"
#> [17] "ERVK" "Helitron" "TcMar-Tc2" "hAT-Blackjack"
#> [21] "TcMar" "SVA_D" "SVA_C" "MamRep605"
#> [25] "hAT" "RTE-BovB" "ERV" "RTE"
#> [29] "LTR" "PiggyBac" "MuDR" "UCON9"
#> [33] "Dong-R4" "telo" "SINE" "centr"
#> [37] "UCON28a" "UCON2" "UCON22" "UCON5"
#> [41] "MamRep564" "UCON31" "SVA_F" "SVA_B"
#> [45] "SVA_E" "SVA_A" "UCON26" "Satellite"
#> [49] "acro" "UCON18" "UCON27" "Penelope"
#> [53] "UCON4" "UCON24" "UCON16" "UCON11"
#> [57] "Merlin" "UCON10" "MER130" "Eulor4"
#> [61] "UCON17" "UCON6" "UCON20" "UCON28c"
#> [65] "UCON8" "UCON1" "UCON19" "UCON28b"
#> [69] "UCON12A" "UCON25" "UCON15" "UCON12"
#> [1] "-------------------------"
#> [1] "Class ID"
#> [1] "========================="
#> [1] "SINE" "DNA" "LTR" "LINE" "RNA" "DNA?"
#> [7] "RC" "SVA" "Unknown" "Satellite" "SINE?" "LTR?"
#> [13] "LINE?" "Unknown?"
#> gene_id family_id class_id
#> 1 AluSx3 Alu SINE
#> 2 MER5A hAT-Charlie DNA
#> 3 MER41B ERV1 LTR
#> 4 MIR MIR SINE
#> 5 AluY Alu SINE
#> 6 MIRb MIR SINE
#> 7 L2a L2 LINE
#> 8 MER77B ERVL LTR
#> 9 LTR44 ERV1 LTR
#> 10 AluJo Alu SINE
#> 11 Tigger2a TcMar-Tigger DNA
#> 12 MLT1C ERVL-MaLR LTR
#> 13 MER1A hAT-Charlie DNA
#> 14 L1MEg L1 LINE
#> 15 AluJr Alu SINE
#> 16 AluSc5 Alu SINE
#> 17 MER5B hAT-Charlie DNA
#> 18 L2c L2 LINE
#> 19 AluSz Alu SINE
#> 20 AluSx1 Alu SINE
#> 21 MIRc MIR SINE
#> 22 L1M5 L1 LINE
#> 23 AluSc Alu SINE
#> 24 MIR3 MIR SINE
#> 25 MER106B hAT-Charlie DNA
#> 26 L1PB3 L1 LINE
#> 27 AluSx Alu SINE
#> 28 L1MA7 L1 LINE
#> 29 L2b L2 LINE
#> 30 LTR78 ERV1 LTR
#> 31 AluJb Alu SINE
#> 32 L1PA5 L1 LINE
#> 33 L1PA11 L1 LINE
#> 34 L1PA4 L1 LINE
#> 35 L1MDa L1 LINE
#> 36 L1MA4 L1 LINE
#> 37 LTR88b Gypsy LTR
#> 38 L1PA8 L1 LINE
#> 39 L3 CR1 LINE
#> 40 L1ME2z L1 LINE
#> 41 FRAM Alu SINE
#> 42 L1PA14 L1 LINE
#> 43 AluYc Alu SINE
#> 44 MLT1G3 ERVL-MaLR LTR
#> 45 MLT2E ERVL LTR
#> 46 AluSg Alu SINE
#> 47 MER41-int ERV1 LTR
#> 48 MER20 hAT-Charlie DNA
#> 49 L1MEe L1 LINE
#> 50 MLT2F ERVL LTR
#> 51 LTR67B ERVL LTR
#> 52 THE1B ERVL-MaLR LTR
#> 53 MamGypLTR2b Gypsy LTR
#> 54 L1PA3 L1 LINE
#> 55 MADE1 TcMar-Mariner DNA
#> 56 Charlie26a hAT-Charlie DNA
#> 57 L1ME4a L1 LINE
#> 58 MLT1B ERVL-MaLR LTR
#> 59 L2 L2 LINE
#> 60 L1MD3 L1 LINE
#> 61 L1PA16 L1 LINE
#> 62 7SK RNA RNA
#> 63 MER45B hAT-Tip100 DNA
#> 64 L1MC L1 LINE
#> 65 AluSg7 Alu SINE
#> 66 MLT1F-int ERVL-MaLR LTR
#> 67 L1MC1 L1 LINE
#> 68 MLT1F ERVL-MaLR LTR
#> 69 MamGypLTR3 Gypsy LTR
#> 70 Eulor5A DNA DNA?
#> 71 AluSq2 Alu SINE
#> 72 AmnSINE2 Deu SINE
#> 73 AluSz6 Alu SINE
#> 74 LTR13A ERVK LTR
#> 75 L1MB8 L1 LINE
#> 76 MLT1J ERVL-MaLR LTR
#> 77 LTR16B1 ERVL LTR
#> 78 LTR16B2 ERVL LTR
#> 79 LTR16B ERVL LTR
#> 80 HAL1 L1 LINE
#> 81 MER45A hAT-Tip100 DNA
#> 82 L1M1 L1 LINE
#> 83 Helitron2Na_Mam Helitron RC
#> 84 MARNA TcMar-Mariner DNA
#> 85 MER91A hAT-Tip100 DNA
#> 86 AluSc8 Alu SINE
#> 87 Kanga1d TcMar-Tc2 DNA
#> 88 L1PB4 L1 LINE
#> 89 FLAM_C Alu SINE
#> 90 MER58C hAT-Charlie DNA
#> 91 MER30 hAT-Charlie DNA
#> 92 ERV3-16A3_I-int ERVL LTR
#> 93 L1MC3 L1 LINE
#> 94 LTR16E1 ERVL LTR
#> 95 L1MEa L1 LINE
#> 96 THE1D ERVL-MaLR LTR
#> 97 L1MB2 L1 LINE
#> 98 L1M4 L1 LINE
#> 99 L1MB5 L1 LINE
#> 100 L1MB3 L1 LINE
#> 101 L1MB4 L1 LINE
#> 102 LTR1 ERV1 LTR
#> 103 AluSp Alu SINE
#> 104 MER63B hAT-Blackjack DNA
#> 105 L1MA8 L1 LINE
#> 106 L1PA17 L1 LINE
#> 107 L1M6 L1 LINE
#> 108 AluSg4 Alu SINE
#> 109 Charlie7a hAT-Charlie DNA
#> 110 MER1B hAT-Charlie DNA
#> 111 MSTA ERVL-MaLR LTR
#> 112 LTR87 ERVL LTR
#> 113 MER135 DNA DNA
#> 114 MER58B hAT-Charlie DNA
#> 115 L1MC4 L1 LINE
#> 116 MER6B TcMar-Tigger DNA
#> 117 Tigger2 TcMar-Tigger DNA
#> 118 L1PA15 L1 LINE
#> 119 MER103C hAT-Charlie DNA
#> 120 L1MCa L1 LINE
#> 121 MLT2B3 ERVL LTR
#> 122 LTR39 ERV1 LTR
#> 123 Tigger1 TcMar-Tigger DNA
#> 124 MER112 hAT-Charlie DNA
#> 125 MamRep1161 TcMar DNA
#> 126 MER4C ERV1 LTR
#> 127 MER11A ERVK LTR
#> 128 LTR8 ERV1 LTR
#> 129 Charlie1b hAT-Charlie DNA
#> 130 LTR32 ERVL LTR
#> 131 MER65D ERV1 LTR
#> 132 MLT1D ERVL-MaLR LTR
#> 133 MER117 hAT-Charlie DNA
#> 134 MLT1A ERVL-MaLR LTR
#> 135 MER51E ERV1 LTR
#> 136 AluJr4 Alu SINE
#> 137 MLT2C1 ERVL LTR
#> 138 L1ME1 L1 LINE
#> 139 L1M7 L1 LINE
#> 140 MLT1A-int ERVL-MaLR LTR
#> 141 LTR5B ERVK LTR
#> 142 L1PA7 L1 LINE
#> 143 L1PA13 L1 LINE
#> 144 MLT2B4 ERVL LTR
#> 145 MLT1F2 ERVL-MaLR LTR
#> 146 MER47B TcMar-Tigger DNA
#> 147 L1MA1 L1 LINE
#> 148 MER84 ERV1 LTR
#> 149 MLT1A0 ERVL-MaLR LTR
#> 150 LTR33 ERVL LTR
#> 151 LTR78B ERV1 LTR
#> 152 Charlie2b hAT-Charlie DNA
#> 153 Arthur1 hAT-Tip100 DNA
#> 154 Charlie2a hAT-Charlie DNA
#> 155 SVA_D SVA_D SVA
#> 156 MER5A1 hAT-Charlie DNA
#> 157 L1PB1 L1 LINE
#> 158 AluYk11 Alu SINE
#> 159 LTR5_Hs ERVK LTR
#> 160 LTR81B Gypsy LTR
#> 161 LTR79 ERVL LTR
#> 162 MER9a1 ERVK LTR
#> 163 MLT1H ERVL-MaLR LTR
#> 164 MER33 hAT-Charlie DNA
#> 165 Charlie7 hAT-Charlie DNA
#> 166 SVA_C SVA_C SVA
#> 167 MER58A hAT-Charlie DNA
#> 168 MER63A hAT-Blackjack DNA
#> 169 MADE2 TcMar-Mariner DNA
#> 170 MER44B TcMar-Tigger DNA
#> 171 Tigger7 TcMar-Tigger DNA
#> 172 Charlie17a hAT-Charlie DNA
#> 173 L1M4b L1 LINE
#> 174 AluSx4 Alu SINE
#> 175 Charlie21a hAT-Charlie DNA
#> 176 Charlie15a hAT-Charlie DNA
#> 177 MamRep605 MamRep605 Unknown
#> 178 L1ME3C L1 LINE
#> 179 LTR83 ERVL LTR
#> 180 Charlie4z hAT-Charlie DNA
#> 181 MLT1J2 ERVL-MaLR LTR
#> 182 FLAM_A Alu SINE
#> 183 Tigger12A TcMar-Tigger DNA
#> 184 L1ME5 L1 LINE
#> 185 L1MD2 L1 LINE
#> 186 L1MB7 L1 LINE
#> 187 L1MEc L1 LINE
#> 188 L1ME3F L1 LINE
#> 189 Tigger15a TcMar-Tigger DNA
#> 190 MamRep137 TcMar DNA
#> 191 MER110 ERV1 LTR
#> 192 L1ME3D L1 LINE
#> 193 LTR27 ERV1 LTR
#> 194 LTR48B ERV1 LTR
#> 195 MER34A1 ERV1 LTR
#> 196 MER31-int ERV1 LTR
#> 197 MER34B-int ERV1 LTR
#> 198 LTR45 ERV1 LTR
#> 199 LTR14B ERVK LTR
#> 200 MLT1E1A ERVL-MaLR LTR
#> 201 MER92C ERV1 LTR
#> 202 LTR37A ERV1 LTR
#> 203 THE1C ERVL-MaLR LTR
#> 204 AluSq Alu SINE
#> 205 AluSq10 Alu SINE
#> 206 MER34A ERV1 LTR
#> 207 LTR6B ERV1 LTR
#> 208 AluYa5 Alu SINE
#> 209 MLT1I-int ERVL-MaLR LTR
#> 210 LTR23 ERV1 LTR
#> 211 MLT1I ERVL-MaLR LTR
#> 212 ERVL-B4-int ERVL LTR
#> 213 MER53 hAT DNA
#> 214 LTR49 ERV1 LTR
#> 215 THE1A ERVL-MaLR LTR
#> 216 MamRep434 TcMar-Tigger DNA
#> 217 L1MC4a L1 LINE
#> 218 L1MC5 L1 LINE
#> 219 MLT1L ERVL-MaLR LTR
#> 220 L1MA4A L1 LINE
#> 221 MER113A hAT-Charlie DNA
#> 222 MER3 hAT-Charlie DNA
#> 223 Tigger12c TcMar-Tigger DNA
#> 224 LTR1D ERV1 LTR
#> 225 MER8 TcMar-Tigger DNA
#> 226 MLT1N2 ERVL-MaLR LTR
#> 227 MER2 TcMar-Tigger DNA
#> 228 MLT1F1 ERVL-MaLR LTR
#> 229 L1PB2 L1 LINE
#> 230 L1MA3 L1 LINE
#> 231 L1M2 L1 LINE
#> 232 MER81 hAT-Blackjack DNA
#> 233 Charlie18a hAT-Charlie DNA
#> 234 AluYf4 Alu SINE
#> 235 Charlie8 hAT-Charlie DNA
#> 236 Charlie22a hAT-Charlie DNA
#> 237 L1MEf L1 LINE
#> 238 MLT1J1 ERVL-MaLR LTR
#> 239 MER90a ERV1 LTR
#> 240 L1PA10 L1 LINE
#> 241 L1ME3 L1 LINE
#> 242 LTR51 ERV1 LTR
#> 243 MSTB ERVL-MaLR LTR
#> 244 MER39 ERV1 LTR
#> 245 Tigger3a TcMar-Tigger DNA
#> 246 MER104 TcMar-Tc2 DNA
#> 247 LTR40a ERVL LTR
#> 248 Tigger16b TcMar-Tigger DNA
#> 249 FAM Alu SINE
#> 250 L1P4 L1 LINE
#> 251 AluSq4 Alu SINE
#> 252 MER66B ERV1 LTR
#> 253 MER31B ERV1 LTR
#> 254 THE1B-int ERVL-MaLR LTR
#> 255 L1MD L1 LINE
#> 256 L1P5 L1 LINE
#> 257 Tigger3d TcMar-Tigger DNA
#> 258 AluYd8 Alu SINE
#> 259 L1M3 L1 LINE
#> 260 AluYg6 Alu SINE
#> 261 L3b CR1 LINE
#> 262 MLT1K ERVL-MaLR LTR
#> 263 X3_LINE RTE-BovB LINE
#> 264 MER5C hAT-Charlie DNA
#> 265 Tigger4b TcMar-Tigger DNA
#> 266 LTR16A1 ERVL LTR
#> 267 LTR24C ERV1 LTR
#> 268 X7C_LINE CR1 LINE
#> 269 Tigger5 TcMar-Tigger DNA
#> 270 LTR10C ERV1 LTR
#> 271 HAL1-3A_ME L1 LINE
#> 272 MER44A TcMar-Tigger DNA
#> 273 MER95 ERV LTR
#> 274 MER34C ERV1 LTR
#> 275 MER21B ERVL LTR
#> 276 MER102c hAT-Charlie DNA
#> 277 L1PREC2 L1 LINE
#> 278 LTR33A ERVL LTR
#> 279 HUERS-P1-int ERV1 LTR
#> 280 ERVL-E-int ERVL LTR
#> 281 MLT2A2 ERVL LTR
#> 282 MER47A TcMar-Tigger DNA
#> 283 MLT2B2 ERVL LTR
#> 284 MLT2B1 ERVL LTR
#> 285 MER83B ERV1 LTR
#> 286 MER52A ERV1 LTR
#> 287 L1ME3E L1 LINE
#> 288 MER21C ERVL LTR
#> 289 MER51A ERV1 LTR
#> 290 MSTB-int ERVL-MaLR LTR
#> 291 MLT1M ERVL-MaLR LTR
#> 292 L4 RTE LINE
#> 293 LTR16C ERVL LTR
#> 294 MER50 ERV1 LTR
#> 295 MER50-int ERV1 LTR
#> 296 MER4D1 ERV1 LTR
#> 297 LTR88c Gypsy LTR
#> 298 MSTD ERVL-MaLR LTR
#> 299 Tigger2b_Pri TcMar-Tigger DNA
#> 300 Plat_L3 CR1 LINE
#> 301 LTR9 ERV1 LTR
#> 302 MSTB1 ERVL-MaLR LTR
#> 303 Charlie24 hAT-Charlie DNA
#> 304 MamRep38 hAT DNA
#> 305 L1MA5A L1 LINE
#> 306 Arthur1A hAT-Tip100 DNA
#> 307 MER124 DNA DNA?
#> 308 MER113 hAT-Charlie DNA
#> 309 MER63C hAT-Blackjack DNA
#> 310 Charlie4a hAT-Charlie DNA
#> 311 X6B_LINE CR1 LINE
#> 312 L1M L1 LINE
#> 313 L1ME2 L1 LINE
#> 314 L1PA6 L1 LINE
#> 315 LTR86B2 ERVL LTR
#> 316 Tigger3b TcMar-Tigger DNA
#> 317 L1MEd L1 LINE
#> 318 ALINE RTE LINE
#> 319 MamRep1527 LTR LTR
#> 320 MER68 ERVL LTR
#> 321 L1MA10 L1 LINE
#> 322 MSTC ERVL-MaLR LTR
#> 323 ORSL-2a hAT-Tip100 DNA
#> 324 MER115 hAT-Tip100 DNA
#> 325 MER75 PiggyBac DNA
#> 326 PRIMA4-int ERV1 LTR
#> 327 PRIMAX-int ERV1 LTR
#> 328 THE1D-int ERVL-MaLR LTR
#> 329 MLT2A1 ERVL LTR
#> 330 HERVL-int ERVL LTR
#> 331 Kanga1c TcMar-Tc2 DNA
#> 332 L1MC2 L1 LINE
#> 333 LTR85b Gypsy LTR
#> [ reached 'max' / getOption("max.print") -- omitted 659 rows ]
# select family
rmskFilter(df, family="hAT-Charlie")
#> gene_id family_id class_id
#> 1 MER5A hAT-Charlie DNA
#> 2 MER1A hAT-Charlie DNA
#> 3 MER5B hAT-Charlie DNA
#> 4 MER106B hAT-Charlie DNA
#> 5 MER20 hAT-Charlie DNA
#> 6 Charlie26a hAT-Charlie DNA
#> 7 MER58C hAT-Charlie DNA
#> 8 MER30 hAT-Charlie DNA
#> 9 Charlie7a hAT-Charlie DNA
#> 10 MER1B hAT-Charlie DNA
#> 11 MER58B hAT-Charlie DNA
#> 12 MER103C hAT-Charlie DNA
#> 13 MER112 hAT-Charlie DNA
#> 14 Charlie1b hAT-Charlie DNA
#> 15 MER117 hAT-Charlie DNA
#> 16 Charlie2b hAT-Charlie DNA
#> 17 Charlie2a hAT-Charlie DNA
#> 18 MER5A1 hAT-Charlie DNA
#> 19 MER33 hAT-Charlie DNA
#> 20 Charlie7 hAT-Charlie DNA
#> 21 MER58A hAT-Charlie DNA
#> 22 Charlie17a hAT-Charlie DNA
#> 23 Charlie21a hAT-Charlie DNA
#> 24 Charlie15a hAT-Charlie DNA
#> 25 Charlie4z hAT-Charlie DNA
#> 26 MER113A hAT-Charlie DNA
#> 27 MER3 hAT-Charlie DNA
#> 28 Charlie18a hAT-Charlie DNA
#> 29 Charlie8 hAT-Charlie DNA
#> 30 Charlie22a hAT-Charlie DNA
#> 31 MER5C hAT-Charlie DNA
#> 32 MER102c hAT-Charlie DNA
#> 33 Charlie24 hAT-Charlie DNA
#> 34 MER113 hAT-Charlie DNA
#> 35 Charlie4a hAT-Charlie DNA
#> 36 Charlie13b hAT-Charlie DNA
#> 37 MER102b hAT-Charlie DNA
#> 38 Charlie5 hAT-Charlie DNA
#> 39 Charlie10 hAT-Charlie DNA
#> 40 Charlie16a hAT-Charlie DNA
#> 41 MER119 hAT-Charlie DNA
#> 42 Charlie10a hAT-Charlie DNA
#> 43 Charlie23a hAT-Charlie DNA
#> 44 Charlie19a hAT-Charlie DNA
#> 45 Charlie9 hAT-Charlie DNA
#> 46 Charlie20a hAT-Charlie DNA
#> 47 MER20B hAT-Charlie DNA
#> 48 Charlie3 hAT-Charlie DNA
#> 49 Charlie1a hAT-Charlie DNA
#> 50 MER106A hAT-Charlie DNA
#> 51 Charlie25 hAT-Charlie DNA
#> 52 MER5C1 hAT-Charlie DNA
#> 53 Charlie13a hAT-Charlie DNA
#> 54 MER102a hAT-Charlie DNA
#> 55 Charlie1 hAT-Charlie DNA
#> 56 MER58D hAT-Charlie DNA
#> 57 Cheshire hAT-Charlie DNA
#> 58 Charlie4 hAT-Charlie DNA
#> 59 MER113B hAT-Charlie DNA
#> 60 Charlie14a hAT-Charlie DNA
#> 61 MER30B hAT-Charlie DNA
#> 62 Charlie6 hAT-Charlie DNA
#> 63 Charlie10b hAT-Charlie DNA
#> 64 Charlie11 hAT-Charlie DNA
#> 65 Charlie1b_Mars hAT-Charlie DNA
#> 66 CheshMITE hAT-Charlie DNA
#> 67 Charlie12 hAT-Charlie DNA
#> 68 Cheshire_Mars_ hAT-Charlie DNA
# select class
df_subset <- rmskFilter(df, class= c("LINE", "SINE"))