This function parses output of seqbuster tool to allow isomiRs/miRNAs analysis of samples in different groups such as characterization, differential expression and clustering. It creates an isomiRs::IsomirDataSeq object.
IsomirDataSeqFromFiles(files, coldata, rate = 0.2, canonicalAdd = TRUE, uniqueMism = TRUE, uniqueHits = FALSE, design = ~1L, minHits = 1L, header = TRUE, skip = 0, quiet = TRUE, ...)
files | files with the output of seqbuster tool |
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coldata | data frame containing groups for each sample |
rate | minimum counts fraction to consider a mismatch a real mutation |
canonicalAdd |
|
uniqueMism |
|
uniqueHits |
|
design | a |
minHits | Minimum number of reads in the sample to consider it in the final matrix. |
header | boolean to indicate files contain headers |
skip | skip first line when reading files |
quiet | boolean indicating to print messages
while reading files. Default |
... | arguments provided to SummarizedExperiment::SummarizedExperiment including rowData. |
IsomirDataSeq class object.
This function parses the output of http://seqcluster.readthedocs.org/mirna_annotation.html for each sample to create a count matrix for isomiRs, miRNAs or isomiRs grouped in types (i.e all sequences with variations at 5' but ignoring any other type). It creates isomiRs::IsomirDataSeq object (see link to example usage of this class) to allow visualization, queries, differential expression analysis and clustering. To create the isomiRs::IsomirDataSeq, it parses the isomiRs files, and generates an initial matrix having all isomiRs detected among samples. As well, it creates a summary for each isomiR type (trimming, addition and substitution) to visualize general isomiRs distribution.
path <- system.file("extra", package="isomiRs") fn_list <- list.files(path, full.names = TRUE) de <- data.frame(row.names=c("f1" , "f2"), condition = c("newborn", "newborn")) ids <- IsomirDataSeqFromFiles(fn_list, coldata=de)#>#> f1 f2 #> hsa-let-7a-5p 0 18 #> hsa-let-7b-5p 0 6 #> hsa-let-7c-5p 0 61 #> hsa-let-7f-5p 8 7 #> hsa-let-7g-5p 74 3 #> hsa-let-7i-5p 0 2