You can download the BALLI R package from this link: [Download]
This is an quick start manual of BALLI
data <- data.frame(read.table("counts.txt"))or make example count data
GenerateData <- function(nRow) {
expr_mean <- runif(1,1,500)
expr_size <- runif(1,1,50)
expr <- rnbinom(20,mu=expr_mean,size=expr_size)
return(expr)
}
data <- data.frame(t(sapply(1:10000,GenerateData)))
colnames(data) <- c(paste0("A",1:10),paste0("B",1:10))
rownames(data) <- paste0("gene",1:10000)
head(data)## A1 A2 A3 A4 A5 A6 A7 A8 A9 A10 B1 B2 B3 B4 B5 B6 B7
## gene1 482 454 408 444 441 344 459 315 525 520 493 468 252 406 259 433 596
## gene2 384 384 214 206 202 163 271 464 617 311 336 151 315 232 334 217 165
## gene3 392 276 369 404 437 337 326 306 496 405 259 390 434 627 252 450 274
## gene4 302 273 281 226 392 234 248 283 383 355 293 244 277 213 277 259 403
## gene5 159 105 149 149 92 105 129 112 117 161 141 186 160 154 162 124 162
## gene6 484 398 402 357 366 376 378 356 490 399 280 411 409 238 449 429 272
## B8 B9 B10
## gene1 490 463 478
## gene2 265 291 454
## gene3 296 388 468
## gene4 237 225 298
## gene5 148 143 158
## gene6 381 398 269## [1] "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "B" "B" "B" "B" "B" "B" "B"
## [18] "B" "B" "B"## (Intercept) GroupB
## 1 1 0
## 2 1 0
## 3 1 0
## 4 1 0
## 5 1 0
## 6 1 0## An object of class "DGEList"
## $counts
## A1 A2 A3 A4 A5 A6 A7 A8 A9 A10 B1 B2 B3 B4 B5 B6 B7
## gene1 482 454 408 444 441 344 459 315 525 520 493 468 252 406 259 433 596
## gene2 384 384 214 206 202 163 271 464 617 311 336 151 315 232 334 217 165
## gene3 392 276 369 404 437 337 326 306 496 405 259 390 434 627 252 450 274
## gene4 302 273 281 226 392 234 248 283 383 355 293 244 277 213 277 259 403
## gene5 159 105 149 149 92 105 129 112 117 161 141 186 160 154 162 124 162
## B8 B9 B10
## gene1 490 463 478
## gene2 265 291 454
## gene3 296 388 468
## gene4 237 225 298
## gene5 148 143 158
## 9995 more rows ...
##
## $samples
## group lib.size norm.factors
## A1 A 2511681 0.9988537
## A2 A 2494483 1.0014121
## A3 A 2520447 0.9974295
## A4 A 2504671 0.9999554
## A5 A 2514640 0.9978297
## 15 more rows ...## An object of class "TecVarList"
## $targets
## group lib.size norm.factors
## A1 A 2508802 0.9988537
## A2 A 2498006 1.0014121
## A3 A 2513968 0.9974295
## A4 A 2504559 0.9999554
## A5 A 2509183 0.9978297
## 15 more rows ...
##
## $design
## (Intercept) GroupB
## 1 1 0
## 2 1 0
## 3 1 0
## 4 1 0
## 5 1 0
## 15 more rows ...
##
## $logcpm
## A1 A2 A3 A4 A5 A6 A7
## gene1 7.591860 7.512082 7.349523 7.476327 7.463942 7.112688 7.521294
## gene2 7.265454 7.271643 6.424942 6.375852 6.345203 6.044347 6.765427
## gene3 7.295048 6.798114 7.205320 7.340762 7.450856 7.083201 7.030223
## gene4 6.920923 6.782460 6.814707 6.508305 7.294831 6.560688 6.638454
## gene5 6.003910 5.420562 5.908469 5.913806 5.227363 5.419455 5.706092
## A8 A9 A10 B1 B2 B3 B4
## gene1 6.983654 7.713922 7.690385 7.621770 7.549161 6.661011 7.340213
## gene2 7.539507 7.946058 6.952524 7.071369 5.930030 6.980665 6.538170
## gene3 6.942101 7.632265 7.331375 6.698399 7.287354 7.440510 7.964696
## gene4 6.830131 7.260978 7.142277 6.875062 6.615158 6.796448 6.416002
## gene5 5.508173 5.567084 6.011292 5.830377 6.227232 6.012177 5.953227
## B5 B6 B7 B8 B9 B10
## gene1 6.692752 7.435331 7.893238 7.617709 7.539468 7.584024
## gene2 7.057150 6.445255 6.052968 6.735881 6.873123 7.510023
## gene3 6.653532 7.490638 6.777773 6.894356 7.285706 7.553650
## gene4 6.788963 6.698371 7.331019 6.576050 6.504903 6.905941
## gene5 6.022433 5.647762 6.026817 5.903988 5.858234 5.999023
## 9995 more rows ...
##
## $tecVar
## A1 A2 A3 A4 A5
## gene1 0.002253682 0.002263340 0.002249089 0.002257467 0.002253343
## gene2 0.003294956 0.003309175 0.003288195 0.003300529 0.003294457
## gene3 0.002642464 0.002653794 0.002637077 0.002646904 0.002642066
## gene4 0.003334766 0.003349157 0.003327923 0.003340406 0.003334261
## gene5 0.007731841 0.007765115 0.007716019 0.007744882 0.007730673
## A6 A7 A8 A9 A10
## gene1 0.002261585 0.002253174 0.002257300 0.002252540 0.002237385
## gene2 0.003306591 0.003294209 0.003300282 0.003293276 0.003270965
## gene3 0.002651735 0.002641869 0.002646708 0.002641125 0.002623348
## gene4 0.003346541 0.003334010 0.003340157 0.003333065 0.003310485
## gene5 0.007759068 0.007730093 0.007744305 0.007727908 0.007675699
## B1 B2 B3 B4 B5
## gene1 0.002325900 0.002329368 0.002328857 0.002321567 0.002316818
## gene2 0.003711364 0.003716936 0.003716114 0.003704401 0.003696772
## gene3 0.002649614 0.002653566 0.002652983 0.002644676 0.002639266
## gene4 0.003630466 0.003635917 0.003635113 0.003623654 0.003616190
## gene5 0.006350003 0.006359509 0.006358107 0.006338124 0.006325108
## B6 B7 B8 B9 B10
## gene1 0.002325856 0.002323898 0.002333473 0.002338612 0.002336599
## gene2 0.003711292 0.003708147 0.003723531 0.003731790 0.003728554
## gene3 0.002649564 0.002647333 0.002658243 0.002664100 0.002661805
## gene4 0.003630396 0.003627319 0.003642369 0.003650448 0.003647282
## gene5 0.006349881 0.006344516 0.006370760 0.006384849 0.006379329
## 9995 more rows ...## An object of class "Balli"
## $Result
## log2FC_GroupB lLLI lBALLI pLLI pBALLI
## gene1 -0.048117429 0.117567614 0.104504549 0.731687730 0.74648953
## gene2 -0.173637988 0.543947455 0.483508915 0.460801362 0.48683721
## gene3 -0.006279292 0.001749189 0.001554835 0.966639552 0.96854645
## gene4 -0.124597847 1.154146485 1.025909151 0.282682824 0.31112143
## gene5 0.279431309 7.198318604 6.398682321 0.007297192 0.01142051
## BCF
## gene1 0.1250000
## gene2 0.1249998
## gene3 0.1250000
## gene4 0.1249987
## gene5 0.1249689
## 9995 more rows ...
##
## $topGenes
## log2FC_GroupB pLLI pBALLI adjpLLI adjpBALLI
## gene8564 -0.5149201 1.478042e-05 4.419314e-05 0.1193062 0.3369298
## gene7284 -0.7208810 2.386125e-05 6.738596e-05 0.1193062 0.3369298
## gene5263 0.3715671 6.543875e-05 1.659905e-04 0.1673996 0.4094708
## gene8864 0.5694819 7.628679e-05 1.916797e-04 0.1673996 0.4094708
## gene1400 -0.9726326 8.369979e-05 2.084111e-04 0.1673996 0.4094708
## 9995 more rows ...