miRetrieve (version 1.3.4)

join_mirtarbase: 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.

Value

Data frame containing miRNA targets.

Details

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

1. 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.

2. 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<U+2013>target interaction database, Nucleic Acids Research, Volume 48, Issue D1, 08 January 2020, Pages D148<U+2013>D154, https://doi.org/10.1093/nar/gkz896

See Also

Other target functions: count_target(), join_targets(), plot_target_count(), plot_target_mir_scatter()