convergentCNV

Options

Option	Description	Argument
--gipOut	GIP output directory [default gipOut]	[char]
--outName	Output name [default gipOut/sampleComparison/convergentCNV]	[char]
--newickTree	Newick tree file produced with the phylogeny module [default gipOut/sampleComparison/phylogeny.treefile]	[char]
--geCNV	Gene CNV excel file produced with the geInteraction module [default gipOut/sampleComparison/geInteraction.CNV.xlsx]	[char]
--ampThresh	Gene normalized coverage amplification threshold [default 1.5]	[double]
--notAmpThresh	Gene normalized coverage threshold below which the gene is considered as not amplified [default 1]	[double]
--covSaturation	Gene normalized coverage saturation value [default 2]	[double]
--treeTip	Color tree tip by this feature. If "NA" tree tips are not colored [default NA]	[char]
--tipLab	Show sample names on the tree tips
--hexpand	Avoid truncating tip labels expanding the plot panel by a ratio of the x axis range [default 0]	[double]
--branchLen	Branch length ggtree parameter [default none]	[branch.length none]
--layout	Layout ggtree parameter [default rectangular]	[rectangular| slanted | circular| fan | daylight]
--hideHeatmap	Do not display the heatmap
--heatCols	Heatmap gradient colors [default black blue white red3 red]	[char …]
--heatMin	Heatmap minimum normalized coverage value [default 0]	[double]
--hideXlabs	Do not display x-axis text
--plotDim	File height and width values [default 6 7]	[double …]
--debug	Dump session and quit

Description

The convergentCNV module is meant to detect convergent CNV gene amplifications. Before running this module the user must first execute the geInteraction and the phylogeny modules to predict the CNV genes and samples phylogeny. For each gene CNV the convergentCNV module identifies the sample pairs (e.g. D and Z) for which the gene is amplified above the normalized coverage threshold (i.e. --ampThresh) and the phylogenetic distance in maximal. Then it evaluates whether there is at least a third sample (e.g. G) not showing the amplification (i.e. normalized coverage < --notAmpThresh) and whose phylogenetic relation is in between the two samples supporting the gene amplification (D and Z). The presence of this intervening sample makes sure that the observed amplification is not explained by a common ancestor. All the geneCNVs fulfilling these sequencing coverage and phylogenetic distance search criteria are selected and used for visualization. Caveat. This module looks for the not-amplified gene just in the samples positioned between the two most distantly related samples showing the amplification (D and Z). Despite unlikely, a given gene CNV could show convergent amplification between samples more closely related and not included in the D to Z range (e.g. A and D) and be left undetected.

Example

From the GIP worked example folder execute

giptools convergentCNV

This will generate the convergentCNV output files in the gipOut/sampleComparison folder.

The convergentCNV.pdf file show the predicted phylogenetic tree side by side with an heatmap showing the normalized gene coverage of the gene CNVS presenting convergent amplifications.

The user can use the --treeTip parameter to color the tree tips according to a feature provided with the --samplesList option of the geInteraction module. For instace running the giptools convergentCNV --treeTip origin command will result in the following plot:

Caveat. The time scale on the tree x axis should not be considered when the --branchLen parameter is equal to “none” (i.e. a cladogram). More in general, the branch length should be taken with caution since the phylogenetic tree is estimated just considering the SNV positions, but not the conserved positions.

The user can remove the x axis labeling by using the --hideXlabs.

The convergentCNV.xlsx file reports the normalized gene coverage of predicted convergent gene CNVs.