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Quick start of BALLI package

Quick Start

This is an quick start manual of BALLI

require(BALLI)

1. Load Count Data

data <- data.frame(read.table("counts.txt"))

or make example count data

##       A1 A2  A3  A4 A5  A6  A7  A8  A9 A10  B1  B2  B3 B4  B5  B6 B7  B8
## gene1  7 39  16  80 48  40 128  48  14  59 160  46  23 63  24 108 40  19
## gene2 33 39 112  24 74  61 167 124  89  95  95 151 206 54 224  66 45 110
## gene3 82 68  39 159 43 103  67 102 182  47  97  97  93 60  74  82 70 109
## gene4 13 18  14  15  6  20  17  11  11   6  13  15   2 12  12  17 13  14
## gene5 10 14  40  26 19  22  19  22  27  20  13   9  17 25  18  12 15  54
## gene6 50 71  20  13 22  10  26  23  10  40  13  22  16 43  42  30 35  43
##       B9 B10
## gene1 22  68
## gene2 75  62
## gene3 56  34
## gene4  5  20
## gene5 16  23
## gene6 26  33

2. Designate Group Information and Make Design Matrix

##  [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

3. Normalize Count Data

## An object of class "DGEList"
## $counts
##       A1 A2  A3  A4 A5  A6  A7  A8  A9 A10  B1  B2  B3 B4  B5  B6 B7  B8
## gene1  7 39  16  80 48  40 128  48  14  59 160  46  23 63  24 108 40  19
## gene2 33 39 112  24 74  61 167 124  89  95  95 151 206 54 224  66 45 110
## gene3 82 68  39 159 43 103  67 102 182  47  97  97  93 60  74  82 70 109
## gene4 13 18  14  15  6  20  17  11  11   6  13  15   2 12  12  17 13  14
## gene5 10 14  40  26 19  22  19  22  27  20  13   9  17 25  18  12 15  54
##       B9 B10
## gene1 22  68
## gene2 75  62
## gene3 56  34
## gene4  5  20
## gene5 16  23
## 9995 more rows ...
## 
## $samples
##    group lib.size norm.factors
## A1     A   551929    0.9939824
## A2     A   554250    1.0019442
## A3     A   551469    0.9964722
## A4     A   551560    1.0071093
## A5     A   546462    0.9998596
## 15 more rows ...

4. Estimate Technical Variance

## An object of class "TecVarList"
## $targets
##    group lib.size norm.factors
## A1     A 548607.7    0.9939824
## A2     A 555327.6    1.0019442
## A3     A 549523.5    0.9964722
## A4     A 555481.2    1.0071093
## A5     A 546385.3    0.9998596
## 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 4.034259 6.206591 5.033024 7.205971 6.515297 6.237959 7.888394
## gene2 5.994961 6.206591 7.696526 5.549376 7.119559 6.822715 8.266935
## gene3 7.258266 6.978131 6.221008 8.179219 6.363232 7.559515 6.974440
## gene4 4.771948 5.171450 4.863019 4.936799 3.868508 5.305636 5.113222
## gene5 4.449749 4.849758 6.255780 5.656237 5.262988 5.431069 5.257693
##             A8       A9      A10       B1       B2       B3       B4
## gene1 6.510839 4.849230 6.797026 8.221498 6.447280 5.477148 6.882641
## gene2 7.844489 7.355990 7.466305 7.481365 8.119834 8.531824 6.667616
## gene3 7.567617 8.371645 6.480929 7.510818 7.491771 7.401550 6.814466
## gene4 4.566359 4.549959 3.864428 4.785661 4.949437 2.844617 4.667364
## gene5 5.451541 5.706648 5.325222 4.785661 4.321116 5.081903 5.615058
##             B5       B6       B7       B8       B9      B10
## gene1 5.559786 7.627629 6.240335 5.251725 5.455301 6.978569
## gene2 8.679625 6.933867 6.402553 7.666884 7.137895 6.849310
## gene3 7.107348 7.238655 7.017734 7.653945 6.728975 6.019453
## gene4 4.666604 5.095240 4.755808 4.859361 3.674976 5.309277
## gene5 5.181240 4.655118 4.936215 6.666856 5.039891 5.493604
## 9995 more rows ...
## 
## $tecVar
##               A1         A2         A3         A4         A5         A6
## gene1 0.02433482 0.02404494 0.02429490 0.02403839 0.02443225 0.02398665
## gene2 0.01290915 0.01276419 0.01288908 0.01276092 0.01295810 0.01273506
## gene3 0.01157954 0.01144914 0.01156159 0.01144619 0.01162334 0.01142290
## gene4 0.06724111 0.06647979 0.06713630 0.06646259 0.06749685 0.06632664
## gene5 0.04159129 0.04110131 0.04152382 0.04109025 0.04175595 0.04100278
##               A7         A8         A9        A10         B1          B2
## gene1 0.02433497 0.02435499 0.02403503 0.02434190 0.01994302 0.019683524
## gene2 0.01290922 0.01291928 0.01275924 0.01291270 0.00991243 0.009788362
## gene3 0.01157961 0.01158861 0.01144467 0.01158272 0.01245367 0.012299260
## gene4 0.06724149 0.06729405 0.06645375 0.06725969 0.07659121 0.075636970
## gene5 0.04159154 0.04162538 0.04108456 0.04160325 0.04821743 0.047601141
##                B3          B4          B5          B6          B7
## gene1 0.019272708 0.019654898 0.019643162 0.019466946 0.019486113
## gene2 0.009591265 0.009774668 0.009769053 0.009684516 0.009693714
## gene3 0.012053776 0.012282216 0.012275228 0.012169979 0.012181437
## gene4 0.074120695 0.075531652 0.075488473 0.074838233 0.074909017
## gene5 0.046619411 0.047532925 0.047504959 0.047083888 0.047129718
##                B8          B9         B10
## gene1 0.019644458 0.019802616 0.019505915
## gene2 0.009769673 0.009845315 0.009703217
## gene3 0.012275999 0.012370146 0.012193274
## gene4 0.075493239 0.076075022 0.074982142
## gene5 0.047508046 0.047884242 0.047177065
## 9995 more rows ...

5. Fit BALLI and See Top Significant Genes

## An object of class "Balli"
## $Result
##       log2FC_GroupB      lLLI    lBALLI      pLLI    pBALLI       BCF
## gene1     0.2862964 0.3791686 0.3370391 0.5380485 0.5615433 0.1249988
## gene2     0.4147916 1.3275686 1.1800625 0.2492382 0.2773433 0.1249985
## gene3    -0.0970422 0.1338105 0.1189427 0.7145134 0.7301840 0.1249997
## gene4    -0.1410062 0.2757014 0.2450759 0.5995326 0.6205638 0.1249635
## gene5    -0.1870295 0.5887311 0.5233292 0.4429102 0.4694250 0.1249728
## 9995 more rows ...
## 
## $topGenes
##          log2FC_GroupB         pLLI       pBALLI   adjpLLI adjpBALLI
## gene6890    -0.8492182 1.197256e-05 3.663179e-05 0.1121975 0.3204511
## gene7128     0.9149524 2.243950e-05 6.409023e-05 0.1121975 0.3204511
## gene3277    -1.2590606 8.539749e-05 2.121336e-04 0.2846583 0.6766089
## gene7092    -1.5531435 1.637869e-04 3.799606e-04 0.3555333 0.6766089
## gene4606     1.4661759 2.563216e-04 5.668673e-04 0.3555333 0.6766089
## 9995 more rows ...

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.