Pipeline askoR: Parameters Table

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
--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