# miRNA Text Mining in Abstracts

## Documentation for package ‘miRetrieve’ version 1.3.4

- DESCRIPTION file.
- Package NEWS.

## Help Pages

add_col_topic | Add topic column to data frame
animal_keywords | Keywords - animals.
assign_topic | Assign topics based on precalculated scores
assign_topic_lda | Assign topics based on LDA model
biomarker_keywords | Keywords - biomarkers.
calculate_score_animals | Calculate animal model scores for abstracts
calculate_score_biomarker | Calculate biomarker scores for abstracts
calculate_score_patients | Calculate patients scores for abstracts
calculate_score_topic | Calculate scores of a self-chosen topic
combine_df | Combine data frames into one data frame
combine_mir | Combine miRNA vectors into one
combine_stopwords | Combine data frames containing stop words
compare_mir_count | Compare count of miRNA names between different topics
compare_mir_count_log2 | Compare log2-frequency count of miRNA names between two topics
compare_mir_count_unique | Compare top count of unique miRNA names per topic
compare_mir_terms | Compare count of terms associated with a miRNA name over various topics
compare_mir_terms_log2 | Compare log2-frequency count of terms associated with a miRNA name
compare_mir_terms_scatter | Compare shared terms associated with a miRNA name
compare_mir_terms_unique | Compare terms uniquely associated with a miRNA name
count_mir | Count miRNA names in a data frame
count_mir_threshold | Count occurrence of miRNA names above threshold
count_snp | Count SNPs in a data frame
count_target | Count targets in data frame
df_crc | Dataset of PubMed data of miRNAs in Colorectal Cancer
df_mirtarbase | miRTarBase version 8.0
df_panc | Dataset of PubMed data of miRNAs in Pancreatic Cancer
df_test | Test dataset of PubMed abstracts
extract_mir_df | Extract miRNA names from abstracts in data frame
extract_mir_string | Extract miRNA names from string
extract_snp | Extract SNPs from abstracts in data frame
fit_lda | Fit LDA-model
generate_stopwords | Generate data frame containing stop words
get_distinct_mir_df | Identify top miRNA names distinct for one topic compared to another topic
get_distinct_mir_vec | Identify miRNA names distinct for one vector compared to another vector
get_mir | Get miRNA names from a data frame
get_pmid | Get PubMed-IDs of a data frame
get_shared_mir_df | Get top miRNA names in common between two topics of a data frame
get_shared_mir_vec | Get miRNA names in common between two vectors
get_snp | Get SNPs from a data frame
indicate_mir | Indicate if a miRNA name is contained in an abstract
indicate_term | Indicate if a term is contained in abstracts
join_mirtarbase | Add miRNA targets from miRTarBase version 8.0
join_targets | Add miRNA targets from an xlsx-file to a data frame
ngram_stopwords | Stop words for n-grams
patients_keywords | Keywords - patients.
plot_lda_term | Plot terms associated with LDA-fitted topics
plot_mir_count | Plot count of most frequently mentioned miRNA names
plot_mir_count_threshold | Plot occurrence count of miRNA names over different thresholds
plot_mir_development | Plot development of miRNA name mentioning over time
plot_mir_new | Plot number of newly mentioned miRNA names/year
plot_mir_terms | Plot count of top terms associated with a miRNA name
plot_perplexity | Plot perplexity score of various LDA models
plot_score_animals | Plot frequency of animal model scores in abstracts
plot_score_biomarker | Plot frequency of biomarker scores in abstracts
plot_score_patients | Plot frequency of patient scores in abstracts
plot_score_topic | Plot frequency of self-chosen topic scores in abstracts
plot_target_count | Plot count of miRNA targets
plot_target_mir_scatter | Plot targets and corresponding miRNAs as a scatter plot
plot_wordcloud | Create wordcloud of terms associated with a miRNA name
read_pubmed | Convert PubMed-file from PubMed into a data frame
read_pubmed_jats | Convert JATS-file from PubMed into a data frame
save_excel | Save data frame(s) as xlsx-file
save_plot | Save the last generated figure
stopwords_2gram | Stop words for text mining with common PubMed 2-grams
stopwords_miretrieve | Stop words for text mining with miRetrieve
stopwords_pubmed | Stop words for text mining from PubMed abstracts
subset_df | Subset data frame for a term
subset_mir | Subset data frame for specific miRNA names
subset_mir_threshold | Subset data frame for miRNA names exceeding a threshold
subset_research | Subset data frame for abstracts of research articles
subset_review | Subset data frame for abstracts of review articles
subset_snp | Subset data frame for specific SNPs
subset_year | Subset data frame for abstracts published in a specific period