Question

How to filter out low read counts

0

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annkolman78 • 0

@annkolman78-21980

Last seen 5.2 years ago

Hi,

I have my data in a SummarizedExperiment format. I would like to filter out reads that have less than 1 read count (exp_count<1)

data

  data class: RangedSummarizedExperiment 
    dim: 56756 100 
    metadata(0):
    assays(10): exp_count TPM ...
      FPKM
      FPKM_CO
    rownames(57736): ENSG00000000003
      ENSG00000000005 ... ENSG00000273492
      ENSG00000273493
    rowData names(9): gene hgncl ...
     colnames(100): 1 1 ...
      99 100
    colData names(13): ID SAMPLE

I have tried:

data_matrix <- data@assays[[1]]
data_filtered <- data_matrix[rowSums(count(data_matrix))>1,]

but got an error:

Error in count(data_matrix) : 
  Argument 'x' must be a vector: numeric

and

data_filtered <- data[rowSums(count(data@assays[[1]]))>1,]

Error in count(data@assays[[1]]) : 
  Argument 'x' must be a vector: numeric

Thank you.

summarizedExperiment • 1.7k views

ADD COMMENT • link updated 5.1 years ago by Martin Morgan 25k • written 5.1 years ago by annkolman78 • 0

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Please NEVER use direct slot access @ and instead use accessors, assay() or assays(data)[[1]].

ADD REPLY • link 5.1 years ago Martin Morgan 25k

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Hi,

Thank you for your reply. I have modified it. What is the reason? But, unfortunatelly it didn't solve the problem.

Thank you

ADD REPLY • link 5.1 years ago annkolman78 • 0

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'Accessors' define how the object is to be manipulated by the user, allowing the developer to chose representations that are efficient for them. For instance, in the Biostrings package

> dna = Biostrings::DNAStringSet("AA")
> dna@<tab>
dna@elementMetadata dna@metadata        dna@ranges
dna@elementType     dna@pool

there is no obvious relationship between operations the user might like to perform and the slots used by the developer to represent the data.

ADD REPLY • link 5.1 years ago Martin Morgan 25k

score 1 · Answer 1 · 2019-10-18

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Martin Morgan 25k

@martin-morgan-1513

Last seen 4 months ago

United States

Note that assays(data)[["exp_count"]] is a matrix, so perhaps you are interested in

keep <- rowSums(assays(data)[["exp_count"]]) > 1
data_filtered <- data[keep,]

ADD COMMENT • link 5.1 years ago Martin Morgan 25k

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Thank you for your answer, I run it and got this error:

Error in assay(data)[["exp_count"]] : 
  subscript out of bounds

ADD REPLY • link 5.1 years ago annkolman78 • 0

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updated assay() --> assays()

ADD REPLY • link 5.1 years ago Martin Morgan 25k

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It is working thank you very much!

ADD REPLY • link 5.1 years ago annkolman78 • 0