## User: vincentpailler

vincentpailler •

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- an hour ago
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- 7 months, 3 weeks ago
- Email:
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... Hello guys,
I want to split my matrix into several submatrices in order to compute the correlations on theses submatrices.
I created an argument `subset` in R which takes into account the number of rows of the matrix.
# get options
option_list = list(
make_option(c("-s" ...

written 1 day ago by
vincentpailler •

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... Hello guys,
I have an output like this :
var1 var2 value
1 OTU0001 OTU0001 1.0000000
2 OTU0004 OTU0001 0.7349885
3 OTU0014 OTU0001 0.5338774
4 OTU0016 OTU0001 0.6671633
5 OTU0017 OTU0001 0.6087571
6 OTU0027 OTU0001 0.5649240
...
I would like to remove ...

written 3 days ago by
vincentpailler •

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Comment:
C: Compute correlations between OTUs

... Thanks a lot for this answer. Do you think it is possible to only get the lower or the upper triangle of the matrix? In order to reduce the time of the script ...

written 7 days ago by
vincentpailler •

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Comment:
C: Compute correlations between OTUs

... I created a small subset with 5 rows and 5 columns.
When I try :
for (i in seq_len(ncol(data)))
{
1-((var(data[,i]-data[,i+1]))/(var(data[,i])+var(data[,i+1])))
}
It returns me an error. The problem is really to create the function which computes "my" formula to compute all correl ...

written 7 days ago by
vincentpailler •

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Comment:
C: Compute correlations between OTUs

... I found this formula in a paper "propr: An R-package for Identifying Proportionally Abundant Features Using Compositional Data Analysis."
I tried :
cores<-32
options('mc.cores'=cores)
registerDoParallel(cores)
data<-read.table("/home/vipailler/PROJET_M2/raw/truelength2. ...

written 7 days ago by
vincentpailler •

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Comment:
C: Compute correlations between OTUs

... I know what you mean, but my main problem is to create this new function.. I checked on Biostars but didn't find anything about my problem.. ...

written 7 days ago by
vincentpailler •

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Comment:
C: Compute correlations between OTUs

... Actually, the problem here is to create the function to compute the correlations between each pairs of OTUs. I do not want to use the function cor() but create the function like I did between the first and the second OTU. I just want to "automatize" this function for each pair ...

written 8 days ago by
vincentpailler •

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... Hi guys,
I've got this kind of matrix : https://ibb.co/r47yY3m
I would like to compute correlations between each pair of OTUs according to this formula (rho coefficient):
https://ibb.co/ky4hkx3
(for example between the first and second OTU)
1-((var(lol[1,]-lol[2,]))/(var(lol[1,])+var(lol ...

written 8 days ago by
vincentpailler •

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... Hello guys,
I want to compute correlations between OTUs (from metagenomic sequencing) . I am working with R and I would like to parallelize the computations because my data set is big.
What I want to do is maybe simple. I work on a cluster with Slurm (I have many CPUs and a lot of memory). I woul ...

written 9 days ago by
vincentpailler •

**50**• updated 9 days ago by Kevin Blighe ♦**39k**1

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... Hi guys,
I explain my problem. I want to compute the scalability of an algorithm on my data set (thousands of rows). For this, I want to subset this data set and increase the size of the subsets of 500rows (so, 1st subset 500 rows, 2nd subset 1000rows, 3rd subset 1500rows...) .
I will use *slurm* ...

written 14 days ago by
vincentpailler •

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