Man pages for alexvpickering/crossmeta
Cross Platform Meta-Analysis of Microarray Data
| add_adjusted | Add expression data adjusted for pairs/surrogate variables |
| addContrastInput | Add contrast input |
| add_sources | Add sample source information for meta-analysis. |
| add_vsd | Add VST normalized assay data element to expression set |
| bulkAnnot | Logic for downloading and uploading bulk annotation |
| bulkAnnotInput | UI for Bulk Data annotation upload/download |
| bulkForm | Logic for Bulk Data form |
| bulkFormInput | Input form for Bulk Data page |
| bulkPage | Logic for Select Contrasts Interface |
| bulkPageUI | UI for Select Contrasts Interface |
| bulkTable | Logic for pdata table |
| bulkTableOuput | Tables for datasets page |
| ch2_subset | Subset for Paired Two-Channel ExpressionSet |
| clean_y | Adjusts expression data for surrogate variables. |
| delContrastsInput | Delete contrasts input |
| diff_expr | Differential expression analysis of esets. |
| es_meta | Effect size combination meta analysis. |
| exprs.MA | Extract Log-Expression Matrix from MAList |
| filter_genes | Filter genes in RNA-seq ExpressionSet |
| fit_ebayes | Fit ebayes model |
| fit_lm | Run limma analysis. |
| fix_illum_headers | Attempts to fix Illumina raw data header |
| format_dl_annot | Format downloaded annotation |
| format_up_annot | Format uploaded annotation |
| get_ch2_mod | Get design matrix for two-channel array |
| get_group_levels | Get group levels for bulk data plots |
| get_palette | Get a Pallete to Distinguish Groups |
| get_raw | Download and unpack microarray supplementary files from GEO. |
| get_sva_mods | Get model matrices for surrogate variable analysis |
| get_top_table | Get top table |
| get_vsd | Get variance stabilized data for exploratory data analysis |
| gslist | KEGG human pathway genes. |
| gs.names | Map between KEGG pathway numbers and names. |
| ilmn.nnum | Count numeric columns in raw Illumina data files |
| iqr_replicates | Removes features with replicated annotation. |
| is_invertible | Check uploaded bulk pdata to make sure the study design is... |
| load_agil_plat | Load Agilent raw data |
| load_diff | Load previous differential expression analyses. |
| load_illum_plat | Illumina loader utility for load_plat. |
| load_plat | Load and pre-process raw Affymetrix, Illumina, and Agilent... |
| load_raw | Load and annotate raw data downloaded from GEO. |
| makeExampleCountsEset | Make example ExpressionSet |
| match_prev_eset | Reuse contrast selections from previous analysis. |
| open_raw_illum | Open raw Illumina microarray files. |
| phenoData.ch2 | Construct AnnotatedDataFrame from Two-Channel ExpressionSet |
| prefix_illum_headers | Run prefix on Illumina raw data files |
| query_ref | Get correlation between query and reference signatures. |
| remove_autonamed | Remove columns that are autonamed by data.table |
| run_limma | Linear model fitting of eset with limma. |
| run_limma_setup | Setup ExpressionSet for running limma analysis |
| run_lmfit | Perform lmFit analysis from limma. |
| run_select_contrasts | Shiny gadget to upload groups and select contrasts |
| run_sva | Run surrogate variable analysis |
| setup_prev | Setup selections when many samples. |
| symbol_annot | Add hgnc symbol to expression set. |
| to_eset | Convert limma object to ExpressionSet |
| to_ma | Covert expression values to MAList |
| validate_up_annot | Validate uploaded bulk annotation |
| which_max_iqr | Get row indices of maximum IQR within annotation groups |
| xls_to_txt | Covert .xls files to .txt |
