Component: ExpressionStats

ExpressionStats

Given an expression matrix and a CSV containing sample IDs and treatment groups, calculate basic statistics by treatment group: mean, median, and standard deviation of genes. Visualizations (histogram, density, boxplot, hierarchical clustering) are generated if parameter makeVisuals is true.

Version	0.1
Bundle	sequencing
Categories	Expression smallRNA
Authors	Katherine Icay (katherine.icay@helsinki.fi), Alejandra Cervera (alejandra.cervera@helsinki.fi)
Issue tracker	View/Report issues
Requires	R ; MASS (R-package) ; ggplot2 (R-package) ; reshape (R-package)
Source files	component.xml ExpressionStats.r
Usage	Example with default values ExpressionStats( expr = CSV, ref = CSV, //geneSet = CSV, //bodyMap = CSV, biotype = "skip", biotype_min = 0, bodySite = "body", exprID = "", makeVisuals = false, refGroup = "Treatment", refID = "", topNum = 10 )

Version

0.1

Bundle

sequencing

Categories

Expression smallRNA

Authors

Katherine Icay (katherine.icay@helsinki.fi), Alejandra Cervera (alejandra.cervera@helsinki.fi)

Issue tracker

View/Report issues

Requires

R ; MASS (R-package) ; ggplot2 (R-package) ; reshape (R-package)

Source files

component.xml ExpressionStats.r

Usage

Example with default values

Inputs

Name	Type	Mandatory	Description
expr	CSV	Mandatory	Expression matrix. If matrix has an additional bio_type column annotated, parameter `biotype` should not be "skip".
ref	CSV	Mandatory	CSV file containing sample names and treatment groups. Sample names must match column names of `expr`.
geneSet	CSV	Optional	2-column list of interesting genes (gene id, gene name) to create heatmap with. Id column should be the same name as defined in parameter `exprID`.
bodyMap	CSV	Optional	Illumina body map. CSV file of geneIds (rows) per tissue (columns). Ids used should be the same as in expr (e.g. Ensembl gene id).

Name

Type

Mandatory

Description

expr

CSV

Mandatory

Expression matrix. If matrix has an additional bio_type column annotated, parameter biotype should not be "skip".

ref

CSV

Mandatory

CSV file containing sample names and treatment groups. Sample names must match column names of expr.

geneSet

CSV

Optional

2-column list of interesting genes (gene id, gene name) to create heatmap with. Id column should be the same name as defined in parameter exprID.

bodyMap

CSV

Optional

Illumina body map. CSV file of geneIds (rows) per tissue (columns). Ids used should be the same as in expr (e.g. Ensembl gene id).

Outputs

Name	Type	Description
stats	CSV	Rows of genes with columns containing the mean, median and standard deviation of its expression by treatment type.
statsArray	Array<CSV>	Additional statistics (topExpressed, topExpressedByTissue, zero, low, high, and summary) when `makeVisuals` is true and `biotype` is not skipped.
report	Latex	Produced only if parameter `makeVisuals` is true. Latex report containing expression visualizations using additional inputs `geneSet` and `bodyMap`.

Name

Type

Description

stats

CSV

Rows of genes with columns containing the mean, median and standard deviation of its expression by treatment type.

statsArray

Array<CSV>

Additional statistics (topExpressed, topExpressedByTissue, zero, low, high, and summary) when makeVisuals is true and biotype is not skipped.

report

Latex

Produced only if parameter makeVisuals is true. Latex report containing expression visualizations using additional inputs geneSet and bodyMap.

Parameters

Name	Type	Default	Description
biotype	string	"skip"	Is bio_type annotation added to input expr file? Either blank "" or "skip". Default is to skip this step.
biotype_min	float	0	When biotype is blank "", this is the minimum expression value to consider when calculating additional statistics.
bodySite	string	"body"	Any body tissue from the Illumina Body Map. Default is an empty string, but other options are heart, stomach, brain, etc.
exprID	string	""	Column name of `expr` file containing the unique gene IDs that statistics are calculated for. If blank, the first column is used.
makeVisuals	boolean	false	Perform additional analysis of geneSet. When true, geneSet and bodyMap should be defined.
refGroup	string	"Treatment"	Column name of `ref` file containing the treatment information corresponding to each sample ID. If blank, the component will lookfor a "Treatment" column.
refID	string	""	Column name of `ref` file containing the reference names to match to the `expr` columns. If blank, the first column is used.
topNum	int	10	Number of top genes to be reported

Name

Type

Default

Description

biotype

string

"skip"

Is bio_type annotation added to input expr file? Either blank "" or "skip". Default is to skip this step.

biotype_min

float

When biotype is blank "", this is the minimum expression value to consider when calculating additional statistics.

bodySite

string

"body"

Any body tissue from the Illumina Body Map. Default is an empty string, but other options are heart, stomach, brain, etc.

exprID

string

Column name of expr file containing the unique gene IDs that statistics are calculated for. If blank, the first column is used.

makeVisuals

boolean

false

Perform additional analysis of geneSet. When true, geneSet and bodyMap should be defined.

refGroup

string

"Treatment"

Column name of ref file containing the treatment information corresponding to each sample ID. If blank, the component will lookfor a "Treatment" column.

refID

string

Column name of ref file containing the reference names to match to the expr columns. If blank, the first column is used.

topNum

int

Number of top genes to be reported

Test cases

Test case	Parameters▼	IN expr	IN ref	IN geneSet	IN bodyMap	OUT stats	OUT statsArray	OUT report
case1	(missing)	expr	ref	(missing)	(missing)	stats	(missing)	(missing)

Test case

Parameters▼

IN
expr

IN
ref

IN
geneSet

IN
bodyMap

OUT
stats

OUT
statsArray

OUT
report

case1

(missing)

expr

ref

(missing)

stats

(missing)

Anduril