R: Add miRNA targets from an xlsx-file to a data frame

join_targets {miRetrieve}

R Documentation

Add miRNA targets from an xlsx-file to a data frame

Description

Add miRNA targets from an external xlsx-file to a data frame.

Usage

join_targets(
  df,
  excel_file,
  col.pmid.excel,
  col.target.excel,
  col.mir.excel = NULL,
  col.pmid.df = PMID,
  col.topic.df = NULL,
  filter_na = TRUE,
  stem_mir_excel = TRUE,
  reduce = FALSE
)

Arguments

`df`	Data frame containing PubMed-IDs that the miRNA targets shall be joined to.
`excel_file`	xlsx-file. xlsx-file containing miRNA targets and PubMed-IDs.
`col.pmid.excel`	String. Column containing PubMed-IDs of the `excel_file`.
`col.target.excel`	String. Column containing targets of the `excel_file`.
`col.mir.excel`	String. Optional. Column containing miRNAs of the `excel_file`. Needed if `reduce = TRUE`.
`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`.
`stem_mir_excel`	Boolean. If `stem_mir_excel = TRUE`, miRNA names provided in `col.mir.excel` are reduced to their stem, e.g. "miR-20a-5p" becomes "miR-20".
`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 an external xlsx-file to a data frame. To add the targets to the data frame, the xlsx-file and the data frame need to have one column in common, such as PubMed-IDs. join_targets() can return two different data frames, regulated by reduce:

If reduce = FALSE, join_targets() adds targets from an excel-file 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_targets() adds targets from an xlsx-file to the data frame in a new column. However, an altered data frame is returned, containing the PubMed-IDs, targets, and miRNAs from the excel-file. For reduce = TRUE to work, the xlsx-file provided must contain a column with miRNA names.

Value