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Question: Polyester - creating simulated reads based on raw count matrix
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gravatar for sseo2
3 months ago by
sseo20
sseo20 wrote:

I am trying to generate some simulated counts based on a pilot data we have to determine if increasing the number of samples will give us more power in our experiments.

I have a matrix of raw counts containing gene names on rows and sample names in columns and from this I want to use create_read_numbers function from polyester to generate additional simulated samples. However this comes up with an error and I can't understand what is wrong with it. Any ideas?

The code I am running is as below

WTveh_poly <- Counts[,c("WTVEH1IP","WTVEH2IP","WTVEH3IP")]
head(WTveh_poly)

WTveh_poly <- subset(WTveh_poly, rowMeans(WTveh_poly) > 1)
params = get_params(WTveh_poly)
custom_readmat = create_read_numbers(mu=params$mu, fit=params$fit,
                                     p0=params$p0, m=dim(WTveh_poly)[1], n=dim(WTveh_poly)[2], 
                                     seed=100000)

then the output is

Generating data from baseline model.
Error in sample.int(length(x), size, replace, prob) : 
  cannot take a sample larger than the population when 'replace = FALSE'

Here is my session info

R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS
 [1] polyester_1.12.0           ballgown_2.8.4             sva_3.24.4                
 [4] BiocParallel_1.10.1        genefilter_1.58.1          mgcv_1.8-18               
 [7] nlme_3.1-131               BiocInstaller_1.26.0       RColorBrewer_1.1-2        
[10] pheatmap_1.0.8             stringr_1.2.0              dplyr_0.5.0               
[13] DESeq2_1.16.1              SummarizedExperiment_1.6.1 DelayedArray_0.2.2        
[16] matrixStats_0.52.2         Biobase_2.36.2             GenomicRanges_1.28.2      
[19] GenomeInfoDb_1.12.0        IRanges_2.10.1             S4Vectors_0.14.1          
[22] BiocGenerics_0.22.0        readr_1.1.1                biomaRt_2.32.0      

 

Thanks in advances 

ADD COMMENTlink written 3 months ago by sseo20
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