miRNA Text Mining in Abstracts
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Documentation for package ‘miRetrieve’ version 1.3.4
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 |