The tabular output of mirtop is compatible with IsomirDataSeq. This function allows to import the data and filter low confidence isomiRs for downstream analysis.

IsomirDataSeqFromMirtop(mirtop, coldata, ...)

Arguments

mirtop

data.frame with the output of mirtop export

coldata

data.frame with the metadata of the samples

...

It supports the same parameters as in IsomirDataSeqFromRawData.

Value

IsomirDataSeq class object.

Details

The output is generated with mirtop export --format isomir.

Examples

library(readr) path <- system.file("extra", "mirtop", package="isomiRs") fn <- list.files(path, full.names = TRUE) de <- data.frame(row.names=c("sample1" , "sample2"), condition = c("cc", "cc")) # mirtop export --format isomir .... IsomirDataSeqFromMirtop(read_tsv(fn), de)
#> Parsed with column specification: #> cols( #> seq = col_character(), #> mir = col_character(), #> mism = col_character(), #> add = col_character(), #> t5 = col_character(), #> t3 = col_character(), #> sample1 = col_double(), #> sample2 = col_double() #> )
#> Warning: Chi-squared approximation may be incorrect
#> Warning: Chi-squared approximation may be incorrect
#> Warning: Chi-squared approximation may be incorrect
#> Warning: Chi-squared approximation may be incorrect
#> Warning: Chi-squared approximation may be incorrect
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#> Warning: Chi-squared approximation may be incorrect
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#> Warning: Chi-squared approximation may be incorrect
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#> Warning: Chi-squared approximation may be incorrect
#> Warning: Chi-squared approximation may be incorrect
#> Warning: Chi-squared approximation may be incorrect
#> Warning: Chi-squared approximation may be incorrect
#> Warning: Chi-squared approximation may be incorrect
#> Warning: Chi-squared approximation may be incorrect
#> Warning: Chi-squared approximation may be incorrect
#> Warning: Chi-squared approximation may be incorrect
#> Warning: Chi-squared approximation may be incorrect
#> Warning: Chi-squared approximation may be incorrect
#> Warning: Chi-squared approximation may be incorrect
#> Warning: Chi-squared approximation may be incorrect
#> Warning: Chi-squared approximation may be incorrect
#> Warning: Chi-squared approximation may be incorrect
#> Warning: Chi-squared approximation may be incorrect
#> Warning: Chi-squared approximation may be incorrect
#> Warning: Chi-squared approximation may be incorrect
#> Warning: Chi-squared approximation may be incorrect
#> Warning: Chi-squared approximation may be incorrect
#> Warning: Chi-squared approximation may be incorrect
#> Warning: Chi-squared approximation may be incorrect
#> Warning: Chi-squared approximation may be incorrect
#> Warning: Chi-squared approximation may be incorrect
#> Warning: Chi-squared approximation may be incorrect
#> Warning: Chi-squared approximation may be incorrect
#> Warning: Chi-squared approximation may be incorrect
#> Warning: Chi-squared approximation may be incorrect
#> Warning: Chi-squared approximation may be incorrect
#> Warning: Chi-squared approximation may be incorrect
#> Warning: Chi-squared approximation may be incorrect
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#> Warning: Chi-squared approximation may be incorrect
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#> Warning: Chi-squared approximation may be incorrect
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#> Warning: Chi-squared approximation may be incorrect
#> Warning: Chi-squared approximation may be incorrect
#> Warning: Chi-squared approximation may be incorrect
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#> Warning: Chi-squared approximation may be incorrect
#> Warning: Chi-squared approximation may be incorrect
#> Warning: Chi-squared approximation may be incorrect
#> Warning: Chi-squared approximation may be incorrect
#> Warning: Chi-squared approximation may be incorrect
#> Warning: Chi-squared approximation may be incorrect
#> Warning: Chi-squared approximation may be incorrect
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#> Warning: Chi-squared approximation may be incorrect
#> Warning: Chi-squared approximation may be incorrect
#> class: IsomirDataSeq #> dim: 66 2 #> metadata(2): sequences rawData #> assays(1): counts #> rownames(66): hsa-let-7a-3p hsa-let-7a-5p ... hsa-miR-93-5p #> hsa-miR-98-5p #> rowData names(0): #> colnames(2): sample1 sample2 #> colData names(1): condition