Man pages for biospi/deamass
Statistical modelling for mass spectrometry omics
| assemble_report-seaMass_sigma-method | Generate html report |
| delta_control-class | Control parameters for seaMass-Δ |
| dinaka | Probability density function of an inverse nakagami... |
| dist_inaka | fit inverse nakagami distribution with fitdistrplus, note our... |
| dist_lst | fit location-scale t distribution with fitdistrplus |
| dist_normal | fit normal distribution with fitdistrplus |
| dist_normal_robust | summarise using median/mad |
| dist_samples_inaka | fit scaled inverse chi distribution |
| dist_samples_lst | fit location-scale t distribution |
| dist_samples_lst_ash | fit location-scale t distribution for ash (minimum df = 2) |
| dist_samples_normal | fit normal distribution with fitdistrplus |
| dist_samples_robust_normal | fit normal distribution with fitdistrplus |
| dist_sf_with_fixed_df1_fitdistrplus | fit scaled F distribution with per-datapoint fixed df1 with... |
| dlst | Probability density function of a location-scale t... |
| generate_markdown-seaMass-method | Generate Rmarkdown for figure |
| import_DIANN | Import DIA-NN data |
| import_MaxQuant | Import MaxQuant LF data |
| import_MaxQuant_evidence0 | Import MaxQuant LF data |
| import_MaxQuant_peptides | Import MaxQuant LF data |
| import_MSqRob | Import MaxQuant LF data |
| import_MSstats | Import data outputed by an MSstats import routine |
| import_OpenSWATH | Import OpenSWATH data |
| import_Progenesis | Import Waters Progenesis data |
| import_ProteinPilot | Import SCIEX ProteinPilot data |
| import_ProteomeDiscoverer | Import Thermo ProteomeDiscoverer data |
| lingofy-seaMass-method | Convert to local lingo |
| new_assay_design | Specify study design for imported dataset |
| pinaka | Cumulative distribution function (CDF) of an inverse nakagami... |
| plot_assay_stdevs-seaMass_sigma-method | #' @import data.table #' @export #' @include generics.R... |
| plot_assay_stdevs-sigma_block-method | #' @import data.table #' @export #' @include generics.R... |
| plot_fdr-seaMass_delta-method | Add together two numbers. |
| plot_pr-seaMass_delta-method | Precision-Recall plot |
| plot_robust_pca-seaMass-method | Plot robust PCA fit |
| plot_volcano-seaMass_delta-method | Volcano plot |
| plst | Cumulative distribution function (CDF) of a location-scale t... |
| qinaka | Quantile function (inverse CDF) of an inverse nakagami... |
| qlst | Quantile function (inverse CDF) of a location-scale t... |
| render_markdown-seaMass-method | Render Rmarkdown |
| rhat | rhat |
| robust_pca-seaMass-method | Robust PCA fit |
| runs | Imported dataset run information |
| schedule_local-class | Schedule seaMass to run locally |
| schedule_pbs-class | Schedule seaMass to run on PBS |
| schedule_sge-class | Schedule seaMass to run on SGE |
| schedule_slurm-class | Schedule seaMass to run on SLURM |
| seaMass-class | seaMass class |
| seaMass_delta-class | seaMass-delta |
| seaMass_group_quants-class | seaMass group quants class |
| seaMass_sigma-class | seaMass-Σ |
| seaMass_theta-class | seaMass-theta |
| sigma_block-class | seaMass-Σ block |
| sigma_control-class | Control parameters for seaMass-Σ |
| squeeze_stdev | Our squeezeVar function - works for small DF unlike Limma... |
| squeeze_stdev_limma | Limma squeezeVar function |
| theta_block-class | seaMass-theta block |
| theta_control-class | Control parameters for seaMass-theta |
