knitr::opts_chunk$set(echo=TRUE, warning=FALSE, message=FALSE)
command line | parameters | default | descriptions |
---------------|-------------------|---------|----------------------------------|
-o
or --out
| parameters$analysis_name
| DE_analysis | Output directory name (do not put space!) |
-d
or --dir
| parameters$dir_path
| "."
| Work directory path |
-O
or --org
| parameters$organism
| 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$regex
| FALSE | Use regex when selecting/removing samples |
-k
or --mk_context
| parameters$mk_context
| FALSE | Generate automatically the context names |
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$heatmap
| TRUE | Generation of the expression heatmap
--nh
| parameters$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
| complete | The agglomeration method to be used : ward.D, ward.D2, single, complete, average, mcquitty, median or centroid
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
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$upset_list
| NULL | Contrast comparison list to display in UpSetR chart
command line | parameters | default | descriptions
--------------|---------------------|----|----------------------------------------|
--GO
| parameters$GO
| NULL | GO enrichment analysis for gene expressed 'up', 'down', 'both', or NULL
--GO_algo
| parameters$GO_algo
| classic | algorithms which are accessible via the runTest function: "whichAlgorithms()"
--GO_stats
| parameters$GO_stats
| fisher | statistical tests which are accessible via the runTest function: "whichTests()"
--GO_cat
| parameters$GO_cat
| BP | GO category to explore: BP, CC or MF
--GO_threshold
| parameters$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
--Ratio_threshold
| parameters$Ratio_threshold
| 0 | the minimum ratio for display GO in graph
command line | parameters | default | descriptions
----------------------------|--------------------------------------|------|---------------------------------------|
--coseq_model
| parameters$coseq_model
| Normal | Coseq model : Poisson, kmeans or Normal
--coseq_normFactors
| parameters$coseq_normFactors
| none | Coseq normalization factor : TC , UQ, Med , DESeq, TMM or none (default none)
--coseq_transformation
| parameters$coseq_transformation
| arcsin | Coseq tranformation : voom, logRPKM, arcsin, logit, logMedianRef, profile, logclr, clr, alr, ilr or none
--coseq_ClustersNb
| parameters$coseq_ClustersNb
| 2:12 | Coseq : number of clusters desired (2:12 (auto), number from 2 to 12)
--coseq_ContrastsThreshold
| parameters$coseq_ContrastsThreshold
| 1 | Coseq : number of contrasts in which DE genes are found for clustering
--coseq_normFactors
| parameters$coseq_normFactors
| none | Coseq normalization factor (TC , UQ, Med , DESeq, TMM , none)
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