calculate_score_biomarker: Calculate biomarker scores for abstracts
In JulFriedrich/miRetrieve: miRNA Text Mining in Abstracts

Description Usage Arguments Details Value See Also

Calculate biomarker score for each abstract to indicate possible use of miRNAs as biomarker.

calculate_score_biomarker(
  df,
  keywords = biomarker_keywords,
  case = FALSE,
  threshold = NULL,
  indicate = FALSE,
  discard = FALSE,
  col.abstract = Abstract
)

`df`	Data frame containing abstracts.
`keywords`	Character vector. Vector containing keywords. The score is calculated based on these keywords. How much weight a keyword in `keywords` carries is determined by how often it is present in `keywords`, e.g. if a keyword is mentioned twice in `keywords` and it is mentioned only once in an abstract, it adds 2 points to the score. The predefined keywords can be accessed via `miRetrieve::biomarker_keywords`.
`case`	Boolean. If `case = TRUE`, terms contained in `keywords` are case sensitive. If `case = FALSE`, terms contained in `keywords` are case insensitive.
`threshold`	Integer. Optional. Threshold to decide if use of miRNAs as biomarker are present in an abstract or not. If `indicate = TRUE` or `discard = TRUE` and `threshold` not specified, `threshold` is automatically set to `1`.
`indicate`	Boolean. If `indicate = TRUE`, an extra column is added. This extra column contains "Yes" or "No", indicating the use of miRNAs as biomarker in abstracts.
`discard`	Boolean. If `TRUE`, only abstracts are kept where miRNAs as biomarker.
`col.abstract`	Symbol. Column containing abstracts.

Calculate biomarker score for each abstract to indicate possible use of miRNAs as biomarker. This score is added to the data frame as an additional column Biomarker_score, containing the calculated biomarker score. To decide which abstracts are considered to contain use of miRNAs as biomarker, a threshold can be set via the threshold argument. Furthermore, an additional column can be added, verbally indicating the general use of miRNAs as biomarker in an abstract. Choosing the right threshold can be facilitated using plot_score_biomarker().

Data frame with calculated biomarker scores. If discard = FALSE, adds extra columns to the original data frame with calculated biomarker scores. If discard = TRUE, only abstracts are with miRNAs as biomarker are kept.

plot_score_biomarker()

Other score functions: assign_topic(), calculate_score_animals(), calculate_score_patients(), calculate_score_topic(), plot_score_animals(), plot_score_biomarker(), plot_score_patients(), plot_score_topic()