R: Add miRNA targets from miRTarBase version 8.0

join_mirtarbase {miRetrieve}

R Documentation

Add miRNA targets from miRTarBase version 8.0

Description

Add miRNA targets from miRTarBase version 8.0 to a data frame.

Usage

join_mirtarbase(
  df,
  col.pmid.df = PMID,
  col.topic.df = NULL,
  filter_na = TRUE,
  reduce = FALSE
)

Arguments

`df`	Data frame containing PubMed-IDs that the miRNA targets shall be joined to.
`col.pmid.df`	Symbol. Column containing PubMed-IDs in `df`.
`col.topic.df`	Symbol. Optional. Only important if `reduce = TRUE`. If given, adds a topic column to the reduced data.frame.
`filter_na`	Boolean. If `filter_na = TRUE`, drops all rows containing `NA` in column `Target`.
`reduce`	Boolean. If `reduce = FALSE`, adds a new column containing miRNA targets to `df`. If `reduce = TRUE`, adds two new columns containing miRNA names and miRNA targets to `df`. All other columns except for the PubMed-ID column and (optionally) the topic column are dropped.

Details

Add miRNA targets from miRTarBase version 8.0 to a data frame. join_mirtarbase() can return two different data frames, regulated by reduce:

If reduce = FALSE, join_mirtarbase() adds targets from miRTarBase 8.0 to the data frame in a new column. These targets then correspond to the targets determined in the research paper, but do not necessarily correspond to the miRNA names mentioned in the abstract.
If reduce = TRUE, join_mirtarbase() adds targets from miRTarBase 8.0 to the data frame in a new column. However, an altered data frame is returned, containing the PubMed-IDs, targets, and miRNAs from miRTarBase 8.0.

miRTarBase was published in

Hsi-Yuan Huang, Yang-Chi-Dung Lin, Jing Li, et al., miRTarBase 2020: updates to the experimentally validated microRNA–target interaction database, Nucleic Acids Research, Volume 48, Issue D1, 08 January 2020, Pages D148–D154, https://doi.org/10.1093/nar/gkz896

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