In askomics/askoR: Differential Expression Analysis using 'edgeR'

knitr::opts_chunk$set(echo=TRUE, warning=FALSE, message=FALSE)

files and samples options

command line | parameters | default | descriptions | ---------------|-------------------|---------|----------------------------------| -o or --out | parameters$analysis_name | DE_analysis | Output directory name (do not put space!) | -d or --dir | parameters$dir_path | "." | Work directory path | -P or --prj | parameters$projectName | Asko | Output files prefix | -f or --fileofcount | parameters$fileofcount | NULL | Matrix of count for all samples/conditions | -G or --col_genes | parameters$col_genes | 1 | Column of genes ids in count files | -C or --col_counts | parameters$col_counts | 7 | Column of counts in count files | -t or --sep | parameters$sep | NULL | Field separator for count files or count matrix | -c or --contrasts | parameters$contrast_file | NULL | Matrix of different contrasts desired | -s or --sample | parameters$sample_file | NULL | File describing the samples | -a or --annotation | parameters$annotation | NULL | File containing the genes' annotations | --ID2GO | parameters$geneID2GO_file | NULL | GO annotation files | -S or --select | parameters$select_sample | NULL | Selected sampls | -r or --remove | parameters$rm_sample | FALSE | Removed samples | -R or --regex | parameters$regex | FALSE | Use regex when selecting/removing samples |

Filter and normalization

command line | parameters | default | descriptions ----------------|-----------------------|-------|-----------------------------------------------| --th_cpm | parameters$threshold_cpm | 0.5 | CPM's threshold --rep | parameters$replicate_cpm | 3 | Minimum of samples pass CPM's threshold --norm_factor | parameters$norm_factor | FALSE | Generate file with normalize factor values --norm_counts | parameters$norm_counts | FALSE | Generate files with mormalized counts --dens_bottom_mar | parameters$densbotmar | 20 | Set bottom margin of density plot to help position the legend --dens_inset | parameters$densinset | 0.45 | Set position the legend in bottom density graphe --legend_col | parameters$legendcol | 6 | Set numbers of column for density plot legends --palette | parameters$palette | Set2 | color palette (ggplot) --hm | parameters$heatmap | TRUE | Generation of the expression heatmap --CompleteHm | parameters$CompleteHeatmap | FALSE | Generation of the normalized expression on ALL genes --nh | parameters$numhigh | 50 | Number of genes in the heatmap --dclust | parameters$distcluts | euclidean | The distance measure to be used : euclidean, maximum, manhattan, canberra, binary or minkowski --hclust | parameters$hclust | ward.D | The agglomeration method to be used : ward.D, ward.D2, single, complete, average, mcquitty, median or centroid

Differential expression analysis

command line | parameters | default | descriptions ------------------|---------------------|-----|--------------------------------------| -n or --normalization | parameters$normal_method | TMN | normalization method (TMM/RLE/ upperquartile/none) --adj | parameters$p_adj_method | fdr | p-value adjust method (holm/hochberg/hommel/ bonferroni/BH/BY/fdr/none) --th_FDR | parameters$threshold_FDR | 0.05 | FDR threshold --glm | parameters$glm | qlf | GLM method (lrt/qlf) --glmDisp | parameters$glm_disp | FALSE | Estimate Common, Trended and Tagwise Negative Binomial dispersions GLMs --lfc | parameters$logFC | TRUE | logFC in the summary table --th_lfc | parameters$threshold_logFC | 1 | logFC threshold --fc | parameters$FC | TRUE | FC in the summary table --lcpm | parameters$logCPM | FALSE | logCPm in the summary table --fdr | parameters$FDR | TRUE | FDR in the summary table --lr | parameters$LR | FALSE | LR in the summary table --sign | parameters$Sign | TRUE | Significance (1/0/-1) in the summary table --expr | parameters$Expression | TRUE | Significance expression in the summary table --mc | parameters$mean_counts | TRUE | Mean counts in the summary table
--plotMD | parameters$plotMD| FALSE | Mean-Difference Plot (aka MA plot) --plotVO | parameters$plotVO | FALSE | Volcano plot --glimMD | parameters$glimMD | FALSE | Glimma - Interactif Mean-Difference Plot (aka MA plot) --glimVO | parameters$glimVO | FALSE | Glimma - Interactif Volcano plot

Venn and Upset graphs

command line | parameters | default | descriptions --------|--------------|---|---------------------------------------| --VD | parameters$VD | NULL | Plot VennDiagram, precise type of comparison: all, down, up or both --compaVD | parameters$compaVD | NULL | Contrast comparison list to display in VennDiagram --upset_basic | parameters$upset_basic | NULL | Display UpSetR charts for all contrasts, precise type of comparison: all, down, up, mixed. --upset_type | parameters$upset_type | NULL | Display UpSetR charts for list of contrasts, precise type of comparison: all, down, up, mixed. --upset_list | parameters$upset_list | NULL | Contrast comparison list to display in UpSetR chart

GOs enrichment analysis

command line | parameters | default | descriptions --------------|---------------------|----|----------------------------------------| --GO | parameters$GO | NULL | GO enrichment analysis for gene expressed 'up', 'down', 'both', or NULL --GO_algo | parameters$GO_algo | weight01 | algorithms which are accessible via the runTest function: "whichAlgorithms()" --GO_stats | parameters$GO_stats | fisher | statistical tests which are accessible via the runTest function: "whichTests()" --GO_threshold | parameters$GO_threshold | 0.05 | the significant threshold used to filter p-values --GO_max_top_terms | parameters$GO_max_top_terms | 10 | the maximum number of GO terms plot --GO_min_num_genes | parameters$GO_min_num_genes | 10 | the minimum number of genes for each GO terms --GO_min_sig_genes | parameters$GO_sig_genes | 1 | the minimum number of significant genes behind the enriched GO-term --Ratio_threshold | parameters$Ratio_threshold | 0 | the minimum ratio for display GO in graph

Co-expression analysis

command line | parameters | default | descriptions ----------------------------|--------------------------------------|------|---------------------------------------| --coseq_data | parameters$coseq_data | ExpressionProfiles | set LogScaledData if you want to clusterize on data in transformed in log (ExpressionProfiles is recommended by coseq creators) --coseq_model | parameters$coseq_model | Normal | Coseq model : Poisson, kmeans or Normal --coseq_transformation | parameters$coseq_transformation | arcsin | Coseq tranformation : voom, logRPKM, arcsin, logit, logMedianRef, profile, logclr, clr, alr, ilr or none --coseq_ClustersNb | parameters$coseq_ClustersNb | 2:25 | number of clusters desired (2:25 number from 2 to 25) --coseq_ContrastsThreshold | parameters$coseq_ContrastsThreshold | 1 | Coseq number of contrasts in which DE genes are found for clustering --coseq_HeatmapOrderSample | parameters$coseq_HeatmapOrderSample | FALSE | Set TRUE if you prefer keeping your sample order than clusterizing samples in heatmap