Man pages for Rundmus/BAf-R_package
Binder Array data hanlding package in facility
| abspqn | Antibody Specific Probabilistic Quotient Normaliation |
| apply_per_group | Apply functions |
| ask_save.plot_QC.SBA | plot for basic QC of SBA data |
| as.matrix.BAf | as.matrix.BAf |
| BAf-class | An S4 class to handle the data from Binder Arrays |
| BAf-package | BAf : A package for handling the data from Binder Arrays in... |
| batch | Access batch IDs |
| boxplot_nEle | Box plot and number |
| cbind_rbind | Combine BAf objects by Rows or Columns |
| combine_repeats | Function to combine repeated measures |
| data_access | Access data stored in a BAf object |
| default_color_SBA_bead | Default color of SBA beads |
| default_color_SBA_ctrl_samples | Default colors of control samples |
| divideBy | divide by a column in @sinfo |
| dot-boxplot_color_tbl | boxplot using color table |
| dot-reorder_BAf_and_replace_0 | reorder sample and replace 0 |
| failed_to_NA | Failed sample/binder to NA |
| hist_correlation | Histogram of correlation |
| key_id_access | Access key ids |
| meanBy | Mean within subset |
| normn_MA | Multi-dimensional MA normalization for plate effect |
| parse_FlexMAP3D_csv_2_list | parse raw file from FLEXMAP3D |
| plateLayout.SBA | Design plate layout |
| plot_a_pair_vectors | Plot to compare a pair of vectors |
| plot_a_pair_vectors_in_MA | MA-plot with coloring by group |
| plot_compareMeanOfEach_inPairs | To compare means in every plates |
| plot_PC | Plot of principal components |
| plot_QC_bead_count_boxplot | Bead count plot |
| plot_QC_binder_corr_hist | Correlation with a binder |
| plot_QC_binder_signal_boxplot | Signal distribution across binders |
| plot_QC_repl_var | Replicates variation plot |
| plot_QC_sample_signal_boxplot | Signal distribution across samples |
| pqn | Probabilistic Quotient Normaliation |
| read_FlexMAP3D_csv | Generate BAf object parsing raw file from FLEXMAP3D |
| read_LIMS_SBA_files | Parse a set of constituent files exported from LIMS for a... |
| read_Olink_excel | Read Olink Excel |
| repeat_indicator | Handle repeat indicator of the key IDs |
| replace_0 | replace 0 with given value |
| sba | data - sba |
| select_filter | Extract like dplyr::select, filter |
| std_curve | Standard curve function |
| sub-BAf-ANY-ANY-ANY-method | Extract a part of data |
| summary | summary of the BAf object |
| transform_to_landscape_for_repeats | Transform to landscape form |
| trim_outlier | Trim outlier out by Robust PCA |
| well_position | Conversion of well position index |
| write_primary_QC_report.SBA | Write primary QC report |
| write_textfiles_to_share | Text files to share |
