R: Get miRNA names from a data frame

get_mir {miRetrieve}

R Documentation

Get miRNA names from a data frame

Description

Get miRNA names from a data frame. These miRNA names can either be the most frequent ones, or the ones exceeding a threshold.

Usage

get_mir(
  df,
  top = NULL,
  threshold = NULL,
  topic = NULL,
  col.mir = miRNA,
  col.pmid = PMID,
  col.topic = Topic
)

Arguments

`df`	Data frame containing miRNA names. If `threshold` is set, `df` must also contain PubMed-IDs. If `topic` is set, `df` must also contain topic names.
`top`	Integer. Optional. Specifies number of most frequent miRNA names to return. If neither `top` nor `threshold` is set, `top` is automatically set to `5`.
`threshold`	Integer or float. Optional. If `threshold` >= 1, return miRNA names mentioned in at least `threshold` abstracts. If `threshold` is between 0 and 1, return miRNA names mentioned in at least `threshold` abstracts of all abstracts in `df`.
`topic`	String. Optional. Character vector specifying which topics to obtain miRNA names from.
`col.mir`	Symbol. Column containing miRNA names.
`col.pmid`	Symbol. Column containing PubMed-IDs.
`col.topic`	Symbol. Column containing topic names.

Details

Get miRNA names from a data frame. These miRNA names can either be the most frequent ones, or the ones exceeding a threshold. Furthermore, if the data frame contains abstracts of different topics, only the miRNA names of specific topics can be obtained by setting the topic argument.

To get the most frequent miRNA names, set the top argument. top determines how many most frequent miRNA names are returned, according to their rank. Ties among the most frequently mentioned miRNAs are treated as the same rank, e.g. if miR-126, miR-34, and miR-29 were all mentioned the most often with the same frequency, they would all be returned by specifying top = 1, top = 2, and top = 3.
To get the miRNA names exceeding a threshold, set the threshold argument. threshold can either be an absolute value, e.g. 3, or a float between 0 and 1, e.g. 0.2. If threshold is an absolute value, get_mir() returns only the miRNA names mentioned in at least threshold abstracts. If threshold is a float between 0 and 1, get_mir() returns only miRNA names mentioned in at least threshold abstracts of all abstracts. threshold requires the data frame to have a column with PubMed IDs.

If neither top nor threshold is set, top is automatically set to 5.

Value