Man pages for lefeverde/lefutils
Robust R functions for common data wrangling tasks
| basic_linear_regression | Function performs lm over accross a number of genes |
| basic_logistic_regression | Performs logistic regression with numerous Y vals |
| better_model_matrix | Creates a much nicer formatted design matrix than the default... |
| clean_by_levels | Removes un-informative cols from a data.frame |
| clean_colnames | Convert Column Names to Lowercase, Replace Whitespace, and... |
| color_dna_sequence | Colors a vector of DNA/peptide sequences via html |
| de_rbind_df | de_rbind_df |
| dge_wrapper | Wrapper function to create dge from txi |
| dice | Calculates the Dice coefficient |
| dot-create_test_dds | Title |
| dot-get_lfc | Gets lfc from a pathway res df |
| dot-lmlist_to_df | Turn summary object from lm into a data.frame |
| dot-split_by_reg | Split a named vector of DEGs by fold change |
| dot-split_fix_names | Split names by delim character |
| enrich_wrapper | Over Representation analysis (ORA) |
| expression_summaries | Returns summaries of gene expression |
| find_na_rows | Finds rows in a data.frame which contain NA values |
| gene_quantile_filter | Gene expression filter by quantile |
| get_deseq2_results | Returns DESeq2 results in long format |
| get_geneSets | Extract genes sets from a pathway results data.frame |
| get_limma_results | get results from limma fit object |
| get_overlap_matix | Creates matrix of overlap ratios |
| increase_xy_lims | Returns expanded coordinates of a ggplot |
| jaccard | Calculates the jaccard distance between 2 named sets |
| make_flextable | Makes a flextable that can be (sometimes, atleast) used as-is |
| order_by_similarity | Order DNA sequences by Levenshtein edit distance |
| overlap_ratio | Calculates the overlap coefficient of 2 sets |
| pca_plotter | Plots PC1 by PC2 using ggplot |
| pipe | Pipe operator |
| rbind_named_df_list | rbinds a named list of data.frames |
| select_genes_by_variance | Selects the top n genes by variance |
| theme_large_font | Increases ggplot2 theme size |
| uniquefy_base | Base function which does the uniquefying |
| uniquefy_by_abs_max | Return a unique data.frame by max value |
| uniquefy_by_variance | Uniquefy by variance |
| venn_maker | Venn maker |
| voom_sva_wrapper | Runs voom to sva pipeline |
| wilcoxOrKruskalOnA | Comparison of distributions of sample groups |
