OmicsSIMLA

File name of the sequence file

A sequence file that contains a population of sequences (or haplotypes)

(include path if not in the OmicsSIMLA directory)

File name of the recombination file

The recombination fraction file is a text file that specifies the recombination fractions for locations in the reference sequences.

(include path if not in the OmicsSIMLA directory)

Do you have a pedigree structure file?

The format in the pedigree structure file is the same as the format in the PLINK fam file.

Yes No

What is the file name of the pedigree structure file (include path if not in the current directory)?

Do you have a proband file

The proband file has the format as the pedigree structure file. A proband file should be used with the pedigree structure file. The individual specified in the proband file should be also in the pedigree structure file.

file?

Yes No

What is the file name of the proband file (include path if not in the current directory)?

What is the name of the folder

OmicsSIMLA will write the simulated files in the specified folder

that OmicsSIMLA will write the simulated files to?

What is the header

For example, study1.ped, study2.ped,…,etc will be generated.

of the simulated files? (ex: study)

How many replicates of simulated data will be generated? (ex: 5000)

How many default 3-generation

The family has a fixed structure with 12 individuals. Please see the user manual for the structure of the default 3-generation families

families will be generated in each replicate? (ex: 100)

How many unrelated cases will be generated in each replicate? (ex: 1000)

How many unrelated controls will be generated in each replicate? (ex: 1000)

Number of parallel threads to run the simulation?

SeqSIMLA options △ Expand CNV option △ Expand pWGBSSimla options △ Expand

Chromosomal region

The region where the CpGs will be simulated

(ex: 1:10000-20000)

Data type

Tissue type

29 tissue types can be simulated

Tissue type

29 tissue types can be simulated

Tissue type

29 tissue types can be simulated

Profile path

Path to the directory where the methylation profiles are placed

Variance in the beta distribution

The variance in the beta distribution to model the variation in methylation rate due to biological and technical variations

Prop. of phase difference

Proportion of blocks with “Methylated” methylation state that will have difference in methylation rates between cases and controls.

in methylated regions

Prop. of phase difference

Proportion of blocks with “Unmethylated” methylation state that will have difference in methylation rates between cases and controls.

in unmethylated regions

Prop. of phase difference

Proportion of blocks with “Fuzzy” methylation state that will have difference in methylation rates between cases and controls

in fuzzy regions

Theta

The difference in methylation probabilities between cases and controls for blocks with phase difference.

Maximum number of differential methylated CpGs per block

Prop

The proportion of methylation blocks with allele-specific methylation

. of allele-specific methylation

Ratio

Ratio of the father-specific methylation rate. Methylation rate for the paternal allele at a CpG will be r_methylated_father*p, where p is the methylation rate for the CpG from the profile.

of paternal methylation

Ratio

Ratio of the mother-specific methylation rate. Methylation rate for the maternal allele at a CpG will be r_methylated_mother*p, where p is the methylation rate for the CpG from the profile.

of maternal methylation

methylation QTL

This option specifies the locations of the meQTLs

(ex: 1,10,25)

Fold change

Fold change of the methylation rate caused by an allele change at the meQTL.

for the meQTL (ex: 0.2,0.3)

Blocks

This option specifically determines the blocks to have the CpGs affected by meQTLs.

affected by meQTLs

Minimum correlation coefficient in block

The minimum correlation coefficient of methylation levels in a block influenced by a meQTL or a block with ASM

RNA-seq options △ Expand

Gene expression profile file

Path to the file where the gene expression profile file is placed

Number of equivalently expressed (EE) genes

Number of differentially expressed (DE) genes

Fold changes

This options specifies the fold changes of gene expression between cases and controls for the DE genes

of the DE genes

Shuffle

When yes is selected, profile of a gene is randomly sampled with replacement from the profiles

the gene expression profiles?

Yes No

Will you simulate eQTL?

Yes No

Please specify the eQTL sites

This option specifies the locations of the eQTLs affecting the EE genes

Please specify the eQTL sites

This option specifies the locations of the eQTLs affecting the DE genes

for the DE genes

Fold changes

This option specifies the fold change for the gene expression of the EE genes affected by eQTL (expression for the genotype at an eQTL relative to the reference genotype at the eQTL)

of the EE genes affected by eQTL

Fold changes

This option specifies the fold change for the gene expression of the DE genes affected by eQTL (expression for the genotype at an eQTL relative to the reference genotype at the eQTL)

of the DE genes affected by eQTL

Will you simulate allele-specific expression?

Yes No

Please specify the cis-eQTL sites

This option specifies the locations of the cis-eQTLs that cause the allele-specific expression (ASE)

The effect size

The effect size is defined as log2(expression of the alternative allele/expression of the reference allele)

of the heterozygous cis-eQTL

Will you simulate expression quantitative trait methylation?

Yes No

Blocks

The block(s) that will contain the eQTM.

containing the eQTM (ex: 12,15)

The proportion of eQTM sites in the total CpGs

Maximum eQTM

The maximum number of eQTM sites in a block

per block

The mean and sd

The effect size of the eQTM will be randomly generated from a normal distribution with a mean and a standard deviation as specified here

for the effect size of the eQTM

The proportion

The proportion of genes influenced by eQTM that will have differential expression between cases and controls

of DE genes influenced by eQTM

Fold change

The fold changes of gene expression influenced by the eQTM in cases relative to controls

of the DE genes influenced by eQTM

Protein expression option △ Expand

Generate Command