Man pages for hammerlab/rinfino
R-friendly client to run infino (http://github.com/hammerlab/infino)
| execute_cibersort | Execute cibersort using Rserve |
| expdata_as_df | convert expdaat (as GxS matrix) to tbl_df format |
| expdata_as_matrix | convert expdata (as GxS tbl_df) to matrix format |
| filter_expdata | helper function to filter gxs expdata more efficiently than... |
| filter_genes | Filter GxS expression data to specific list of genes If... |
| filter_gxs_expdata | helper function to filter gxs expdata more efficiently than... |
| genelist | Selected genes for use with infino models |
| load_all_expdata | load several expdata files all at once |
| load_expdata | loads expression data in GxS format, with one row per gene &... |
| load_lm22_genes | Helper function to load lm22 genes from cibersort_home and... |
| merge_expdata | merge expdata dfs together, combining sampleinfo |
| prep_expression_matrix | Prepare expression matrix of transcript- or gene-specific... |
| rcctils_expression | Gene expression matrices for TILs isolated from RCC patients... |
| rcctils_sampleinfo | Sample info for TILs isolated from RCC patients (E-MTAB-5640) |
| run_cibersort | Run cibersort on expression data |
| run_combat | Run combat to normalize for batch effects |
| run_estimate | Run estimate on expression data |
| run_pca | run PCA analysis on expression data |
| shell | Helper to execute shell commands (linux) |
| singleorigin_expression | Gene expression matrices for immune cells isolated from PBMC... |
| singleorigin_sampleinfo | Sample info for immune cells isolated from PBMC samples... |
| test_cibersort | Test cibersort using one of the expression matrices provided |
| transform_cibersort_to_relative | Transform 'Absolute' mode of cibersort results to relative... |
| transform_sampleid | Transform sample_id in both expdata & in attributes |
| transpose2gxs | Function to transpose an SxG df of expression data into GxS... |
| transpose2sxg | Function to transpose an GxS df of expression data into SxG... |
| transpose_expdata | helper function to transpose a dataframe of expression data... |
| update_sampleinfo | Update sampleinfo affiliated with expdata |
