mirtop
output into IsomirDataSeq
IsomirDataSeqFromMirtop.Rd
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, ...)
mirtop | data.frame with the output of |
---|---|
coldata | data.frame with the metadata of the samples |
... | It supports the same parameters as in IsomirDataSeqFromRawData. |
IsomirDataSeq class object.
The output is generated with mirtop export --format isomir
.
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)#>#> #>#> 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#> 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#> 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#> 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