Question

Error of PWM not colsum to 1 from package DiffLogo or seqLogo

1

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zhxiaokang ▴ 20

@zhxiaokang-13311

Last seen 2.3 years ago

Norway

I am using the package DiffLogo to plot seqlogo. If I understand correctly, it's like an extension of the package seqLogo. I am using the former one just because it provides the function to take FASTA file and compute the PWM. I got the PWM and confirmed that all the columns' sum is 1. But I still got the compaint that the columns do not sum to 1.

> colSums(pwm)
  1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19  20
  1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1
 21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39  40
  1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1
 41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59  60
  1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1
 61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79  80
  1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1
 81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 100
  1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1
101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120
  1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1
121
  1
> seqLogo(pwm)
[1] "pwm must be of class matrix or data.frame. Trying to convert"
Error in preconditionPWM(pwm) : Columns of PWM must add up to 1.0
In addition: Warning message:
In matrix(pwm, alphabet$size, length(pwm)/alphabet$size) :
  data length [4961] is not a sub-multiple or multiple of the number of rows [4]

> sessionInfo( )
R version 4.1.3 (2022-03-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /home/m320480/.conda/envs/crisprngs/lib/libblas.so.3.9.0
LAPACK: /home/m320480/.conda/envs/crisprngs/lib/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] DiffLogo_2.18.0 cba_0.2-21      proxy_0.4-27

loaded via a namespace (and not attached):
[1] compiler_4.1.3

I also realized that there is a similar question here: -Inf content in a Position Weight Matrix But the only answer there doesn't help to solve my issue.

seqLogo DiffLogo • 1.2k views

ADD COMMENT • link 2.3 years ago zhxiaokang ▴ 20

0

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We need to have access to the pwm object to help you.

ADD REPLY • link 2.3 years ago Guillaume Devailly ▴ 60

0

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I saved the whole workspace on my Google Drive and it can be downloaded here: workspace on GoogleDrive, and the script is here: script on GoogleDrive

ADD REPLY • link 2.3 years ago zhxiaokang ▴ 20

0

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From the warning, looks like you might be starting with a non-base matrix. Try converting first and inspect that object. E.g.,

pwm2 <- as.matrix(pwm)
all(colSums(pwm2) == 1.0)

ADD REPLY • link 2.3 years ago merv ▴ 140

0

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It seems not helping:

> pwm2 <- as.matrix(pwm)
> all(colSums(pwm2) == 1.0)
[1] TRUE
> seqLogo(pwm2)
[1] "pwm must be of class matrix or data.frame. Trying to convert"
Error in preconditionPWM(pwm) : Columns of PWM must add up to 1.0
In addition: Warning message:
In matrix(pwm, alphabet$size, length(pwm)/alphabet$size) :
  data length [4961] is not a sub-multiple or multiple of the number of rows [4]

ADD REPLY • link 2.3 years ago zhxiaokang ▴ 20