calculate_score_biomarker {miRetrieve}

Calculate biomarker scores for abstracts

Description

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

Usage

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

Arguments

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.

Details

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().

Value

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.

See Also

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()