# [R] Calculating all possible ratios

Fri Oct 5 12:28:41 CEST 2012

```Hello,

Comment out the second apply and all following instructions using 'r2'.
In the end return 'r1', not cbind.

Hope this helps,

Em 04-10-2012 23:38, genome1976 escreveu:
> Hi Rui,
>
> A while ago you helped me with calculaing all possible ratios from a dataset.
>
> This is the code I am using as suggested by you.
>
> pairwise.ratios <- function(x, prefix="probeset", char=":"){
>          n <- ncol(x)
>          cn <- colnames(x)
>          if(length(cn) == 0){
>                  cn <- gsub(" ", "0", formatC(seq.int(n), width=nchar(n)))
>                  cn <- paste(prefix, cn, sep="")
>          }
>          cmb <- combn(n, 2)
>          r1 <- apply(cmb, 2, function(j) x[, j[1]]/x[, j[2]])
>          r2 <- apply(cmb, 2, function(j) x[, j[2]]/x[, j[1]])
>          colnames(r1) <- apply(cmb, 2, function(j) paste(cn[j], collapse=char))
>          colnames(r2) <- apply(cmb, 2, function(j) paste(cn[rev(j)], collapse=char))
>          cbind(r1, r2)[, order(c(colnames(r1), colnames(r2)))]
> }
> results <- pairwise.ratios(data.t)
> write.table(t(results), "ratios_results.txt", sep="\t")
>
> It works perfectly fine only that it gives both pairs of ratios a:b and b:a for any two variables a and b.
> Can you suggest me a way so that I get only one ratio and not both (Combination with caring for the order and not Permutation??)
>
> Thanks for any help.
>
> Best Regards,
> Som.
>
>
>
>
>
> Date: Sat, 12 May 2012 15:20:52 -0700
> From: ml-node+s789695n4629656h97 at n4.nabble.com
> To: genome1976 at hotmail.com
> Subject: RE: Calculating all possible ratios
>
> Hello,
>
> Nothing wrong with me, maybe your R session has some conflicting objects.
> Running the function in the previous post on the first 4 rows and first 6 columns of your dataset the result was (copy&paste to your session)
>
> result <- structure(c(8.74714923153198, 1.83094400392095, 9.92065138471113,
> 1.77145415014708, 1.01515180575001, 0.167175438316099, 0.222321656865252,
> 0.155576771874649, 3.09417748158541, 0.469647988505747, 1.29398633565582,
> 0.524043736521509, 3.75969597954255, 0.422694576901317, 9.75471698113208,
> 0.290397651827521, 4.9035575319622, 1.00105273231888, 1.01093964697178,
> 0.26895145631068, 0.114322960947685, 0.546166347992352, 0.100799832714726,
> 0.564507977763338, 0.11605516024473, 0.0913055986191245, 0.0224099858208782,
> 0.0878243288779063, 0.353735531392494, 0.256505926724138, 0.130433606169248,
> 0.295826869963301, 0.42981957664441, 0.230861553382365, 0.983273839877614,
> 0.163931791180376, 0.56058921623124, 0.546741314958369, 0.10190254729944,
> 0.151825242718447, 0.9850743448771, 5.98173996175908, 4.49798734905118,
> 6.4276947512815, 8.61659229879359, 10.9522309159971, 44.6229644227777,
> 11.3863665430362, 3.04799485560622, 2.8093121408046, 5.82033416762497,
> 3.36839317468124, 3.70358005398494, 2.52844904226946, 43.8765935747068,
> 1.86658746243623, 4.83036872336483, 5.98803713273998, 4.54719374273333,
> 1.72873786407767, 0.323187666496628, 2.12925430210325, 0.772805687699305,
> 1.90823767237023, 2.82697074863659, 3.89854539725884, 7.66673581578674,
> 3.38035554418724, 0.328084543240185, 0.35595902124055, 0.1718114409242,
> 0.296877457036954, 1.21508737036511, 0.900024246342843, 7.53850076491586,
> 0.554147739185128, 1.58476931628683, 2.13149583692219, 0.781259909100518,
> 0.513223300970874, 0.265978952936953, 2.36577437858509, 0.102514506769826,
> 3.44355401535389, 2.32655759378615, 4.33160041310018, 1.01701068353905,
> 6.10009805175427, 0.270009014365446, 0.395499368696959, 0.0227911949977918,
> 0.535737017484743, 0.822986086753186, 1.11108117816092, 0.132652370966651,
> 1.8045729131197, 1.30424309801742, 2.36826490573261, 0.103635979283374,
> 0.926148867313916, 0.203933571388086, 0.998948374760994, 0.989178733859585,
> 3.71814309436142, 1.78383738225087, 1.82901853699522, 9.81329737579089,
> 6.58652001534723, 0.207023533247665, 0.166999632405824, 0.219915855047535,
> 0.578456699988768, 0.631006664328306, 0.469154094827586, 1.27998376513563,
> 1.9484696000908, 0.76672822844154, 0.422250060615857, 9.64915859255482,
> 1.07974002376127), .Dim = c(4L, 30L), .Dimnames = list(c("S1",
> "S2", "S3", "S4"), c("P1:P2", "P1:P3", "P1:P4", "P1:P5", "P1:P6",
> "P2:P1", "P2:P3", "P2:P4", "P2:P5", "P2:P6", "P3:P1", "P3:P2",
> "P3:P4", "P3:P5", "P3:P6", "P4:P1", "P4:P2", "P4:P3", "P4:P5",
> "P4:P6", "P5:P1", "P5:P2", "P5:P3", "P5:P4", "P5:P6", "P6:P1",
> "P6:P2", "P6:P3", "P6:P4", "P6:P5")))
>
>
>
>
>
> genome1976 wrote
> Hi Rui,
> Thanks once again. I really appreciate it.
> I tried using the code with the following dataset:
>
>
>
>
>
>
>    Sample
>    P1
>    P2
>    P3
>    P4
>    P5
>    P6
>    P7
>    P8
>    P9
>    P10
>
>
>    S1
>    5292.9
>    605.1
>    5213.9
>    1710.6
>    1407.8
>    1079.4
>    1379.6
>    9321.4
>    6951
>    1205.8
>
>
>    S2
>    104.6
>    57.129
>    625.69
>    222.72
>    247.46
>    104.49
>    330.29
>    1863.7
>    389.67
>    216.29
>
>
>    S3
>    191.29
>    19.282
>    860.42
>    147.83
>    19.61
>    189.22
>    203.27
>    1799
>    369.9
>    175.73
>
>
>    S4
>    41.553
>    23.457
>    267.09
>    79.293
>    143.09
>    154.5
>    52.567
>    613.54
>    408.86
>    61.715
>
>
>    S5
>    671.33
>    19.076
>    1040.9
>    319.04
>    50.766
>    57.445
>    50.005
>    1615.5
>    1149.1
>    163.99
>
>
>    S6
>    125.9
>    22.296
>    563.83
>    236.36
>    112.38
>    81.581
>    48.406
>    2073.6
>    388.4
>    62.575
>
>
>    S7
>    78.485
>    18.152
>    248.18
>    156.19
>    322.4
>    162.01
>    38.379
>    2786.8
>    630.63
>    71.163
>
>
>    S8
>    1355.6
>    51.534
>    422.51
>    134.89
>    202.34
>    48.368
>    69.45
>    231.11
>    1875.9
>    153.18
>
>
>    S9
>    2167.6
>    45.244
>    430.73
>    262.19
>    365.71
>    116.49
>    65.663
>    151.04
>    3071.5
>    210.55
>
>
>    S10
>    575.7
>    24.699
>    170.09
>    128.64
>    42.58
>    31.034
>    55.256
>    294.67
>    448.05
>    226.19
>
>
>    S11
>    234.22
>    22.594
>    944.54
>    118.91
>    16.994
>    102.67
>    199.32
>    2300
>    192.38
>    108.3
>
>
>    S12
>    193.38
>    25.374
>    829.88
>    74.872
>    108.1
>    116.49
>    175.49
>    1248
>    340.33
>    65.022
>
>
>    S13
>    60.43
>    15.907
>    947.23
>    49.12
>    62.992
>    189.11
>    27.348
>    134.46
>    209.66
>    67.638
>
>
>    S14
>    94.563
>    23.304
>    303.25
>    36.745
>    220.11
>    128.72
>    33.242
>    135.6
>    263.31
>    107.4
>
>
>    S15
>    44.379
>    17.794
>    768
>    26.144
>    49.329
>    103
>    26.782
>    290.04
>    151.63
>    66.928
>
>
>    S16
>    42.333
>    14.671
>    224.49
>    19.642
>    100.96
>    82.624
>    42.736
>    94.781
>    182.99
>    68.087
>
>
>    S17
>    528.59
>    49.81
>    685.29
>    24.981
>    106.7
>    72.219
>    114.44
>    610.74
>    1779.9
>    245.57
>
>
> When I run the code, this is what I get :
>
>       probeset1:probeset2 probeset1:probeset3 probeset1:probeset4
> [1,]           0.2000000           0.1111111          0.07692308
> [2,]           0.3333333           0.2000000          0.14285714
> [3,]           0.4285714           0.2727273          0.20000000
> [4,]           0.5000000           0.3333333          0.25000000
>       probeset1:probeset5 probeset1:probeset6 probeset2:probeset1
> [1,]          0.05882353          0.04761905            5.000000
> [2,]          0.11111111          0.09090909            3.000000
> [3,]          0.15789474          0.13043478            2.333333
> [4,]          0.20000000          0.16666667            2.000000
>       probeset2:probeset3 probeset2:probeset4 probeset2:probeset5
> [1,]           0.5555556           0.3846154           0.2941176
> [2,]           0.6000000           0.4285714           0.3333333
> [3,]           0.6363636           0.4666667           0.3684211
> [4,]           0.6666667           0.5000000           0.4000000
>       probeset2:probeset6 probeset3:probeset1 probeset3:probeset2
> [1,]           0.2380952            9.000000            1.800000
> [2,]           0.2727273            5.000000            1.666667
> [3,]           0.3043478            3.666667            1.571429
> [4,]           0.3333333            3.000000            1.500000
>       probeset3:probeset4 probeset3:probeset5 probeset3:probeset6
> [1,]           0.6923077           0.5294118           0.4285714
> [2,]           0.7142857           0.5555556           0.4545455
> [3,]           0.7333333           0.5789474           0.4782609
> [4,]           0.7500000           0.6000000           0.5000000
>       probeset4:probeset1 probeset4:probeset2 probeset4:probeset3
> [1,]                  13            2.600000            1.444444
> [2,]                   7            2.333333            1.400000
> [3,]                   5            2.142857            1.363636
> [4,]                   4            2.000000            1.333333
>       probeset4:probeset5 probeset4:probeset6 probeset5:probeset1
> [1,]           0.7647059           0.6190476           17.000000
> [2,]           0.7777778           0.6363636            9.000000
> [3,]           0.7894737           0.6521739            6.333333
> [4,]           0.8000000           0.6666667            5.000000
>       probeset5:probeset2 probeset5:probeset3 probeset5:probeset4
> [1,]            3.400000            1.888889            1.307692
> [2,]            3.000000            1.800000            1.285714
> [3,]            2.714286            1.727273            1.266667
> [4,]            2.500000            1.666667            1.250000
>       probeset5:probeset6 probeset6:probeset1 probeset6:probeset2
> [1,]           0.8095238           21.000000            4.200000
> [2,]           0.8181818           11.000000            3.666667
> [3,]           0.8260870            7.666667            3.285714
> [4,]           0.8333333            6.000000            3.000000
>       probeset6:probeset3 probeset6:probeset4 probeset6:probeset5
> [1,]            2.333333            1.615385            1.235294
> [2,]            2.200000            1.571429            1.222222
> [3,]            2.090909            1.533333            1.210526
> [4,]            2.000000            1.500000            1.200000
>
>
> As you can see P1:P2 is not 0.2000000 as indicated by the results of the code.
>
> Am I doing something wrong?
>
> Thanks once again.
> Som.
>
> Date: Sat, 12 May 2012 14:04:11 -0700
> From: [hidden email]
> To: [hidden email]
> Subject: RE: Calculating all possible ratios
>
>
>
>          Hello,
>
>
>
>
> pairwise.ratios <- function(x, prefix="probeset", char=":"){
>
>          n <- ncol(x)
>
>          cn <- colnames(x)
>
>          if(length(cn) == 0){
>
>                  cn <- gsub(" ", "0", formatC(seq.int(n), width=nchar(n)))
>
>                  cn <- paste(prefix, cn, sep="")
>
>          }
>
>          cmb <- combn(n, 2)
>
>          r1 <- apply(cmb, 2, function(j) x[, j[1]]/x[, j[2]])
>
>          r2 <- apply(cmb, 2, function(j) x[, j[2]]/x[, j[1]])
>
>          colnames(r1) <- apply(cmb, 2, function(j) paste(cn[j], collapse=char))
>
>          colnames(r2) <- apply(cmb, 2, function(j) paste(cn[rev(j)], collapse=char))
>
>          cbind(r1, r2)[, order(c(colnames(r1), colnames(r2)))]
>
> }
>
>
> m1 <- matrix(1:24, ncol=6)
>
> pairwise.ratios(m1)
>
>
>
>
> genome1976 wrote
> Thanks so much Rui. I really appreciate all the help.
>
>
> I implemented the code and it ran fine. I was wondering how I could include the probeset ids as probeset1:probeset2 in the final output so that I know which ratios are for which probeset pairs.
>
>
>
> Thanks so much.
>
> Som.
>
> Date: Sat, 12 May 2012 09:29:54 -0700
>
> From: [hidden email]
> To: [hidden email]
> Subject: Re: Calculating all possible ratios
>
>
>
>
>          Hello,
>
>
>
> If by all possible gene ratios you mean all pairwise column ratios, try
>
>
> the following.
>
>
>
> # Make up some data
>
>
> x <- matrix(1:24, ncol=6)
>
>
>
> cmb <- combn(ncol(x), 2)
>
>
> r1 <- apply(cmb, 2, function(j) x[, j[1]]/x[, j[2]])
>
>
> r2 <- apply(cmb, 2, function(j) x[, j[2]]/x[, j[1]])
>
>
> cbind(r1, r2)
>
>
>
> Note that the dataset must be a numeric only matrix or data.frame.
>
>
>
> Hope this helps,
>
>
>
>
>
>
> Em 12-05-2012 11:00, [hidden email] escreveu:
>
>
>> Date: Fri, 11 May 2012 12:39:23 -0700 (PDT)
>
>> From: genome1976<[hidden email]>
>
>> To:[hidden email]
>
>> Subject: [R] Calculating all possible ratios
>
>> Message-ID:<[hidden email]>
>
>> Content-Type: text/plain
>
>
>> I have a data matrix with  genes as columns and samples as rows. I want to
>
>> create all possible gene ratios.Is there an elegant and fast way to do it in
>
>> R and write it to a dataframe?
>
>
>> Thanks for any help.
>
>> Som.
>
>
>> --
>
>> View this message in context:http://r.789695.n4.nabble.com/Calculating-all-possible-ratios-tp4627405.html
>> Sent from the R help mailing list archive at Nabble.com.
>
>> [[alternative HTML version deleted]]
>
>
> ______________________________________________
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>                  http://r.789695.n4.nabble.com/Calculating-all-possible-ratios-tp4627405p4629105.html
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>                  NAML
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>                  http://r.789695.n4.nabble.com/Calculating-all-possible-ratios-tp4627405p4629513.html
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>                  NAML
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> NAML
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> --
> View this message in context: http://r.789695.n4.nabble.com/Calculating-all-possible-ratios-tp4627405p4645098.html
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