Component: SignatureExtractor

SignatureExtractor

This component performs signature extraction from point mutation data using non-negative matrix factorization following the pipeline in SomaticSignature R package.

Version	1.2
Bundle	sequencing
Categories	Analysis
Authors	Amjad Alkodsi (Amjad.Alkodsi@Helsinki.FI)
Issue tracker	View/Report issues
Requires	SomaticSignatures (R-bioconductor) ; BSgenome.Hsapiens.UCSC.hg19 (R-bioconductor) ; BSgenome.Hsapiens.UCSC.hg38 (R-bioconductor) ; pheatmap (R-package) ; plyr (R-package) ; cowplot (R-package) ; RColorBrewer (R-package) ; reshape (R-package) ; grid (R-package) ; ggplot2 (R-package)
Source files	component.xml SignatureExtractor.R
Usage	Example with default values SignatureExtractor( in = CSV, altColumn = "alt", barplotDimensions = "5,5", barplotExtra = "", chrColumn = "chr", genomeBuild = "hg19", n = 3, nRange = "2:10", nRep = 5, nrun = 1, posColumn = "pos", refColumn = "ref", sampleIDcolumn = "ID", signaturePlotDimensions = "5,5", signaturePlotExtra = "", sortBy = "burden" )

Version

1.2

Bundle

sequencing

Categories

Analysis

Authors

Amjad Alkodsi (Amjad.Alkodsi@Helsinki.FI)

Issue tracker

View/Report issues

Requires

SomaticSignatures (R-bioconductor) ; BSgenome.Hsapiens.UCSC.hg19 (R-bioconductor) ; BSgenome.Hsapiens.UCSC.hg38 (R-bioconductor) ; pheatmap (R-package) ; plyr (R-package) ; cowplot (R-package) ; RColorBrewer (R-package) ; reshape (R-package) ; grid (R-package) ; ggplot2 (R-package)

Source files

component.xml SignatureExtractor.R

Usage

Example with default values

Name	Type	Mandatory	Description
in	CSV	Mandatory	Input csv file having variant data. The file should have columns for chr, position, ref, alt and sample ID columns that can be specified by parameters

Name

Type

Mandatory

Description

CSV

Mandatory

Input csv file having variant data. The file should have columns for chr, position, ref, alt and sample ID columns that can be specified by parameters

Outputs

Name	Type	Description
outContribution	CSV	CSV file having percentage of contribution of each signature in each sample.
outNmuation	CSV	CSV file having estimated number of mutations induced by each signature in each sample.
signatureDistance	CSV	CSV file having euclidean distance between each extracted signature and the list of published signatures.
plots	BinaryFolder	Binary folder having different plots.

Name

Type

Description

outContribution

CSV

CSV file having percentage of contribution of each signature in each sample.

outNmuation

CSV

CSV file having estimated number of mutations induced by each signature in each sample.

signatureDistance

CSV

CSV file having euclidean distance between each extracted signature and the list of published signatures.

plots

BinaryFolder

Binary folder having different plots.

Parameters

Name	Type	Default	Description
altColumn	string	"alt"	Name of the column having alternative allele
barplotDimensions	string	"5,5"	Dimenstions of the barplot pdf in the format of "width,height".
barplotExtra	string	""	ggplot R expression to be added to barplot command for example 'scale_fill_manual(values=c("red","blue","green")' to change colors.
chrColumn	string	"chr"	Name of column having chromosomes.
genomeBuild	string	"hg19"	Can be either hg19 or hg38.
n	int	3	Final number of signatures to be extracted
nRange	string	"2:10"	R expression for range of number of signatures to be tested for explained variance.
nRep	int	5	Number of repeitition for each number of signatures as specified in the nRange parameter.
nrun	int	1	The signatures will be extracted based on repeated runs specified by this parameter.
posColumn	string	"pos"	Name of column having chromosomal position of the variant.
refColumn	string	"ref"	Name of the column having reference allele.
sampleIDcolumn	string	"ID"	Name of the column having sample IDs.
signaturePlotDimensions	string	"5,5"	Dimenstions of the signature plot pdf in the format of "width,height".
signaturePlotExtra	string	""	ggplot R expression to be added to signature plot command for example 'theme(axis.text.x=element_text(size=5))' to change x axis font size.
sortBy	string	"burden"	sort samples in the barplot according to this parameters. It can take signature names like S1, S2 ..Sn or "burden" to sort by number of mutations.

Name

Type

Default

Description

altColumn

string

"alt"

Name of the column having alternative allele

barplotDimensions

string

"5,5"

Dimenstions of the barplot pdf in the format of "width,height".

barplotExtra

string

ggplot R expression to be added to barplot command for example 'scale_fill_manual(values=c("red","blue","green")' to change colors.

chrColumn

string

"chr"

Name of column having chromosomes.

genomeBuild

string

"hg19"

Can be either hg19 or hg38.

int

Final number of signatures to be extracted

nRange

string

"2:10"

R expression for range of number of signatures to be tested for explained variance.

nRep

int

Number of repeitition for each number of signatures as specified in the nRange parameter.

nrun

int

The signatures will be extracted based on repeated runs specified by this parameter.

posColumn

string

"pos"

Name of column having chromosomal position of the variant.

refColumn

string

"ref"

Name of the column having reference allele.

sampleIDcolumn

string

"ID"

Name of the column having sample IDs.

signaturePlotDimensions

string

"5,5"

Dimenstions of the signature plot pdf in the format of "width,height".

signaturePlotExtra

string

ggplot R expression to be added to signature plot command for example 'theme(axis.text.x=element_text(size=5))' to change x axis font size.

sortBy

string

"burden"

sort samples in the barplot according to this parameters. It can take signature names like S1, S2 ..Sn or "burden" to sort by number of mutations.

Test cases

Test case	Parameters▼	IN in	OUT outContribution	OUT outNmuation	OUT signatureDistance	OUT plots
case1	properties	in	(missing)	(missing)	(missing)	(missing)
	nRange=2:3, nRep=2,

Test case

Parameters▼

IN
in

OUT
outContribution

OUT
outNmuation

OUT
signatureDistance

OUT
plots

case1

properties

(missing)

nRange=2:3,
nRep=2,

Anduril

SignatureExtractor

Inputs

Outputs

Parameters

Test cases