IsomirDataSeq: Class that contains all isomiRs annotation for all samples

In lpantano/isomiRs: Analyze isomiRs and miRNAs from small RNA-seq

Class that contains all isomiRs annotation for all samples

Description

The IsomirDataSeq is a subclass of SummarizedExperiment. used to store the raw data, intermediate calculations and results of an miRNA/isomiR analysis. This class stores all raw isomiRs data for each sample, processed information, summary for each isomiR type, raw counts, normalized counts, and table with experimental information for each sample.

Details

IsomirDataSeqFromFiles creates this object using seqbuster output files.

Methods for this objects are counts() to get count matrix and isoSelect() for miRNA/isomiR selection. Functions available for this object are isoCounts() for count matrix creation, isoNorm() for normalization, isoDE() for differential expression. isoPlot() helps with basic expression plot.

metadata contains one list:

• rawData is a data.frame with the information of each sequence found in the data and the counts for each sample.

The naming of isomiRs follows these rules:

• miRNA name

• type:ref if the sequence is the same as the miRNA reference. iso if the sequence has variations.

• ⁠iso_5p tag⁠:indicates variations at 5 position. The naming contains two words: direction - nucleotides, where direction can be UPPER CASE NT (changes upstream of the 5 reference position) or LOWER CASE NT (changes downstream of the 5 reference position). 0 indicates no variation, meaning the 5 position is the same as the reference. After direction, it follows the nucleotide/s that are added (for upstream changes) or deleted (for downstream changes).

• ⁠iso_3p tag⁠:indicates variations at 3 position. The naming contains two words: direction - nucleotides, where direction can be LOWER CASE NT (upstream of the 3 reference position) or UPPER CASE NT (downstream of the 3 reference position). 0 indicates no variation, meaning the 3 position is the same as the reference. After direction, it follows the nucleotide/s that are added (for downstream changes) or deleted (for upstream chanes).

• ⁠iso_add tag⁠:indicates nucleotides additions at 3 position. The naming contains two words: direction - nucleotides, where direction is UPPER CASE NT (upstream of the 5 reference position). 0 indicates no variation, meaning the 3 position has no additions. After direction, it follows the nucleotide/s that are added.

• ⁠iso_snv tag⁠: indicates nucleotides substitutions along the sequences. The naming contains three words: position-nucleotide@isomiR-nucleotide@reference.

• ⁠iso_snv_seed tag⁠: same as iso_snv tag, but only if the change happens between nucleotide 2 and 8.

In general nucleotides in UPPER case mean insertions respect to the reference sequence, and nucleotides in LOWER case mean deletions respect to the reference sequence.

Examples

path <- system.file("extra", package="isomiRs")
fn_list <- list.files(path, pattern="mirna", full.names = TRUE)
de <- data.frame(row.names=c("f1" , "f2"),
                 condition = c("newborn", "newborn"))
ids <- IsomirDataSeqFromFiles(fn_list, coldata=de)

head(counts(ids))

lpantano/isomiRs documentation built on Aug. 26, 2024, 3:34 a.m.