Pseudomarker statistics

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Pseudomarker specifications


Unique identifier OMICS_07100
Name Pseudomarker
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB
Computer skills Advanced
Stability Stable
Maintained No


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Publication for Pseudomarker

Pseudomarker in publications

PMCID: 3879234
PMID: 24391526
DOI: 10.1371/journal.pgen.1004085

[…] the original cross dataset and the peptidomic analyses were collected at the princeton mass spectrometry facility; all other data were collected in house., genome-wide scans were performed using pseudomarker to detect qtls associated with metabolite levels in the hb3×dd2 genetic cross. intensities of mass signals were log-transformed and the median signal for each mass across replicates […]

PMCID: 3538336
PMID: 23316443
DOI: 10.1534/g3.112.003806

[…] protocol as with the ril population and interpreting the nil results with caution allowed for ease of comparison between the three seed populations., the genomic position, associated marker or pseudomarker, estimated additive effect of substitution of a cvi allele at the indicated locus, and percentage of explained variance for each qtl present in the selected model with the highest lod […]

PMCID: 3320613
PMID: 22509142
DOI: 10.1371/journal.pgen.1002631

[…] to produce estimates of total fecundity., qtl mapping was performed with estimates of total fecundity for each ril (see for details) using multiple imputation with 50 imputations per marker/pseudomarker and a pseudomarker step size of 3cm. we tested for association between genomic location and fecundity by fitting the full model, y = mi+e+mi:e+ε, and the reduced model, y = e+ε, where y […]

PMCID: 3170002
PMID: 21918629
DOI: 10.2147/AABC.S9240

[…] to the model . for each phenotype, qtl positions xqtl and effects bqtl were generated for a model with d qtl, 2 ≤ d ≤ 6 (see below). a(xqtl) was built, using exact genotype information from the pseudomarker simulation, and yqtl = a(xqtl) bqtl was computed. the noise vector ∈ was constructed as the sum of two components, ∈ = ∈gen + ∈rand. the genotype dependent component ∈gen was simulated […]

PMCID: 2553844
PMID: 18828674
DOI: 10.1371/journal.pbio.0060238

[…] massachusetts) was used to generate relative gene expression heat maps., for each expression trait, interval mapping linkage analysis was performed using the bayesian approach implemented in the pseudomarker v2.03 package [] executed in matlab (the mathworks, natick, massachusetts). marker genotypes were used directly (i.e., imputation of “pseudomarkers” was not necessary given […]

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Pseudomarker institution(s)
The Jackson Laboratory, Bar Harbor, ME, USA

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