Arguments

Call Example:

// minimum
dotnet mspc.dll -i rep1.bed -i rep2.bed -r bio -s 1E-8 -w 1E-4

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dotnet mspc.dll -?

Arguments Quick Reference

Argument	Required	Short arg	Valid Values	Default Value
Input	✓	-i	BED file	none
Replicate Type	✓	-r	bio, tec	none
Stringency threshold	✓	-s	double	none
Weak threshold	✓	-w	double	none
Gamma		-g	double	Stringency threshold
C		-c	int	1
Alpha		-a	double	0.05
Multiple Intersections		-m	lowest, highest	lowest
Degree of Parallelism		-d	int	Maximum allowed by the underlying scheduler
Input Parser Configuration		-p	File path	none
Output path		-o	Directory path	session_ + <Timestamp>
Exclude Header				False (not provided)

Arguments

In the following we explain arguments in details.

Input

Sample files are listed after the -i or --input argument.

Short	Long	Required	Valid values	Default value
-i	--input	✓	BED file	none

Example:

dotnet mspc.dll -i rep1.bed -i rep2.bed -i rep3.bed -r bio -w 1e-4 -s 1e-8

You may also pass the input files space-delimited:

dotnet mspc.dll -i rep1.bed rep2.bed rep3.bed -r bio -w 1e-4 -s 1e-8

Wildcard characters can be used to specify multiple files; for instance:

# read all the files with .bed extension as input:
$ dotnet mspc.dll -i *.bed -r bio -w 1e-4 -s 1e-8

# read multiple set of files in different directories:
$ dotnet mspc.dll -i C:\setA\*.bed -i C:\setB\sci-ATAC*.bed -r bio -w 1e-4 -s 1e-8

info

By default, MSPC reads input files unstranded, if your data are stranded, you may adjust the parser accordingly.

Replicate Type

Samples could be biological or technical replicates. MSPC differentiates between the two replicate types based on the fact that less variations between technical replicates is expected compared to biological replicates. Replicate type can be specified using the following argument:

Short	Long	Required	Valid values	Default value
-r	--replicate	✓	Bio, Biological, Tec, Technical	none

Example:

dotnet mspc.dll -i rep1.bed -i rep2.bed -r tec -w 1e-4 -s 1e-8
dotnet mspc.dll -i rep1.bed -i rep2.bed -r biological -w 1e-4 -s 1e-8

Weak Threshold

It sets a threshold on p-values, such that peaks with p-value between this and stringency threshold, are considered weak peaks.

Short	Long	Required	Valid values	Default value
-w	--tauW	✓	Double	none

Example:

dotnet mspc.dll -i rep1.bed -i rep2.bed -r bio -w 1e-4 -s 1e-8

Stringency Threshold

It sets a threshold on p-values, where peaks with p-value lower than this threshold, are considered stringent.

Short	Long	Required	Valid values	Default value
-s	--tauS	✓	Double	none

Example:

dotnet mspc.dll -i rep1.bed -i rep2.bed -r bio -w 1e-4 -s 1e-8

Gamma

It sets the combined stringency threshold. Peaks with combined p-value below this threshold are confirmed.

Short	Long	Required	Valid values	Default value
-g	--gamma	Optional	Double	Equal to Stringency Threshold

Example:

dotnet mspc.dll -i rep1.bed -i rep2.bed -r bio -w 1e-4 -s 1e-8 -g 1e-8

C

It sets the minimum number of overlapping peaks required before MSPC combines their p-value. For example, given three replicates (rep1, rep2 and rep3), if C = 3, a peak on rep1 must overlap with at least two peaks, one from rep2 and one from rep3, before MSPC combines their p-value; otherwise, MSPC discards the peak. If C = 2, a peak on rep1 must overlap with at least one peak from either rep2 or rep3, before MSPC combines their p-values; otherwise MSPC discards the peak.

Short	Long	Required	Valid values	Default value
-c		Optional	String	1

The value of C can be given in absolute (e.g., C = 2 will require at least 2 samples) or percentage of input samples (e.g., C = 50% will require at least 50% of input samples) formats.

The minimum value of C is 1. If a value less than 1 is given (e.g., C = 0, C = 0%, or C = -1), MSPC automatically sets it to 1 (i.e., C = 1).

Example:

dotnet mspc.dll -i rep1.bed -i rep2.bed -r bio -w 1e-4 -s 1e-8 -c 2

dotnet mspc.dll -i rep1.bed -i rep2.bed -r bio -w 1e-4 -s 1e-8 -c 50%

Note, you do not need to enclose a value for C in " to represent it as a string; the values are automatically considered as string type objects. In other words, you do not need to enter the value as C "3".

Alpha

It sets the threshold for Benjamini-Hochberg multiple testing correction.

Short	Long	Required	Valid values	Default value
-a	--alpha	Optional	Double	0.05

Example:

dotnet mspc.dll -i rep1.bed -i rep2.bed -r bio -w 1e-4 -s 1e-8 -a 0.05

Multiple Intersections

When multiple peaks from a sample overlap with a given peak, this argument defines which of the peaks to be considered: the one with lowest p-value, or the one with highest p-value?

Short	Long	Required	Valid values	Default value
-m	--multipleIntersections	Optional	Lowest, Highest	Lowest

Example:

dotnet mspc.dll -i rep1.bed -i rep2.bed -r bio -w 1e-4 -s 1e-8 -m lowest

Degree of Parallelism

It sets the number of parallel threads MSPC can utilize simultaneously when processing data.

Short	Long	Required	Valid values	Default value
-d	--degreeOfParallelism	Optional	int	Number of logical processors on the current machine

Example:

dotnet mspc.dll -i rep1.bed -i rep2.bed -r bio -w 1e-4 -s 1e-8 -d 12

Input Parser Configuration

Sets the path to a JSON file containing the configuration for the input BED file parser.

Short	Long	Required	Valid values	Default value
-p	--parser	Optional	File path	none

Refer to this page on how to configure the input parser using a JSON object.

Output Path

Sets the path in which analysis results should be persisted. If it is not given, the default folder is name session_ + <Timestamp>. If a given folder name already exists, and is not empty, MSPC will append _n where n is an integer until no duplicate is found. See the Output page on the contents of this folder.

Short	Long	Required	Valid values	Default value
-o	--output	Optional	Directory path	session_ + <Timestamp>

Exclude Header

This is a flag (i.e., it does not require any value), if provided, MSPC does not add a header to the files it generates. If not provided (default), MSPC will add a header to all the files it generates.

Short	Long	Required	Valid values	Default value
	--excludeHeader	Optional		False (not provided)

Example:

dotnet mspc.dll --excludeHeader
dotnet mspc.dll --excludeHeader true
dotnet mspc.dll --excludeHeader false