COSDA-UPC - COmpositional and Spatial Data Analysis
http://hdl.handle.net/2117/79720
Sat, 18 Sep 2021 09:10:14 GMT2021-09-18T09:10:14ZA network algorithm for the X chromosomal exact test for Hardy–Weinberg equilibrium with multiple alleles
http://hdl.handle.net/2117/343817
A network algorithm for the X chromosomal exact test for Hardy–Weinberg equilibrium with multiple alleles
Graffelman, Jan; Ortoleva, Leonardo
Statistical methodology for testing the Hardy-Weinberg equilibrium at X chromosomal variants has recently experienced considerable development. Up to a few years ago, testing X chromosomal variants for equilibrium was basically done by applying autosomal test procedures to females only. At present, male alleles can be taken into account in asymptotic and exact test procedures for both the bi-and multiallelic case. However, current X chromosomal exact procedures for multiple alleles rely on a classical full enumeration algorithm and are computationally expensive, and in practice not feasible for more than three alleles. In this article, we extend the autosomal network algorithm for exact Hardy-Weinberg testing with multiple alleles to the X chromosome, achieving considerable reduction in computation times for multiallelic variants with up to five alleles. The performance of the X chromosomal network algorithm is assessed in a simulation study. Beyond four alleles, a permutation test is, in general, the more feasible approach. A detailed description of the algorithm is given, and examples of X chromosomal indels and microsatellites are discussed.
Fri, 16 Apr 2021 09:58:21 GMThttp://hdl.handle.net/2117/3438172021-04-16T09:58:21ZGraffelman, JanOrtoleva, LeonardoStatistical methodology for testing the Hardy-Weinberg equilibrium at X chromosomal variants has recently experienced considerable development. Up to a few years ago, testing X chromosomal variants for equilibrium was basically done by applying autosomal test procedures to females only. At present, male alleles can be taken into account in asymptotic and exact test procedures for both the bi-and multiallelic case. However, current X chromosomal exact procedures for multiple alleles rely on a classical full enumeration algorithm and are computationally expensive, and in practice not feasible for more than three alleles. In this article, we extend the autosomal network algorithm for exact Hardy-Weinberg testing with multiple alleles to the X chromosome, achieving considerable reduction in computation times for multiallelic variants with up to five alleles. The performance of the X chromosomal network algorithm is assessed in a simulation study. Beyond four alleles, a permutation test is, in general, the more feasible approach. A detailed description of the algorithm is given, and examples of X chromosomal indels and microsatellites are discussed.A likelihood ratio approach for identifying three-quarter siblings in genetic databases
http://hdl.handle.net/2117/343815
A likelihood ratio approach for identifying three-quarter siblings in genetic databases
Galván Femenía, Iván; Barceló Vidal, Carles; Sumoy, Lauro; Moreno Aguado, Victor Raul; de Cid, Rafael; Graffelman, Jan
The detection of family relationships in genetic databases is of interest in various scientific disciplines such as genetic epidemiology, population and conservation genetics, forensic science, and genealogical research. Nowadays, screening genetic databases for related individuals forms an important aspect of standard quality control procedures. Relatedness research is usually based on an allele sharing analysis of identity by state (IBS) or identity by descent (IBD) alleles. Existing IBS/IBD methods mainly aim to identify first-degree relationships (parent–offspring or full siblings) and second degree (half-siblings, avuncular, or grandparent–grandchild) pairs. Little attention has been paid to the detection of in-between first and second-degree relationships such as three-quarter siblings (3/4S) who share fewer alleles than first-degree relationships but more alleles than second-degree relationships. With the progressively increasing sample sizes used in genetic research, it becomes more likely that such relationships are present in the database under study. In this paper, we extend existing likelihood ratio (LR) methodology to accurately infer the existence of 3/4S, distinguishing them from full siblings and second-degree relatives. We use bootstrap confidence intervals to express uncertainty in the LRs. Our proposal accounts for linkage disequilibrium (LD) by using marker pruning, and we validate our methodology with a pedigree-based simulation study accounting for both LD and recombination. An empirical genome-wide array data set from the GCAT Genomes for Life cohort project is used to illustrate the method.
Fri, 16 Apr 2021 09:49:47 GMThttp://hdl.handle.net/2117/3438152021-04-16T09:49:47ZGalván Femenía, IvánBarceló Vidal, CarlesSumoy, LauroMoreno Aguado, Victor Raulde Cid, RafaelGraffelman, JanThe detection of family relationships in genetic databases is of interest in various scientific disciplines such as genetic epidemiology, population and conservation genetics, forensic science, and genealogical research. Nowadays, screening genetic databases for related individuals forms an important aspect of standard quality control procedures. Relatedness research is usually based on an allele sharing analysis of identity by state (IBS) or identity by descent (IBD) alleles. Existing IBS/IBD methods mainly aim to identify first-degree relationships (parent–offspring or full siblings) and second degree (half-siblings, avuncular, or grandparent–grandchild) pairs. Little attention has been paid to the detection of in-between first and second-degree relationships such as three-quarter siblings (3/4S) who share fewer alleles than first-degree relationships but more alleles than second-degree relationships. With the progressively increasing sample sizes used in genetic research, it becomes more likely that such relationships are present in the database under study. In this paper, we extend existing likelihood ratio (LR) methodology to accurately infer the existence of 3/4S, distinguishing them from full siblings and second-degree relatives. We use bootstrap confidence intervals to express uncertainty in the LRs. Our proposal accounts for linkage disequilibrium (LD) by using marker pruning, and we validate our methodology with a pedigree-based simulation study accounting for both LD and recombination. An empirical genome-wide array data set from the GCAT Genomes for Life cohort project is used to illustrate the method.Evaluation of natural background levels of high mountain karst aquifers in complex hydrogeological settings. A Gaussian mixture model approach in the Port del Comte (SE, Pyrenees) case study
http://hdl.handle.net/2117/338201
Evaluation of natural background levels of high mountain karst aquifers in complex hydrogeological settings. A Gaussian mixture model approach in the Port del Comte (SE, Pyrenees) case study
Herms Canellas, Joan Ignasi; Jódar, Jorge; Soler, Albert; Lambán, Javier; Custodio Gimena, Emilio; Nuñez, Joan Agustí; Arnó, Georgina; Ortego Martínez, María Isabel; Parcerisa Duocastella, David; Jorge, Joan
Wed, 10 Feb 2021 09:20:02 GMThttp://hdl.handle.net/2117/3382012021-02-10T09:20:02ZHerms Canellas, Joan IgnasiJódar, JorgeSoler, AlbertLambán, JavierCustodio Gimena, EmilioNuñez, Joan AgustíArnó, GeorginaOrtego Martínez, María IsabelParcerisa Duocastella, DavidJorge, JoanSome thoughts on counts in sequencing studies
http://hdl.handle.net/2117/337113
Some thoughts on counts in sequencing studies
Egozcue Rubí, Juan José; Graffelman, Jan; Ortego Martínez, María Isabel; Pawlowsky Glahn, Vera
Measurements in sequencing studies are mostly based on counts. There is a lack of theoretical developments for the analysis and modelling of this type of data. Some thoughts in this direction are presented, which might serve as a seed. The main issues addressed are the compositional character of multinomial probabilities and the corresponding representation in orthogonal (isometric) coordinates, and modelling distributions for sequencing data taking into account possible effects of amplification techniques.
Tue, 09 Feb 2021 08:57:45 GMThttp://hdl.handle.net/2117/3371132021-02-09T08:57:45ZEgozcue Rubí, Juan JoséGraffelman, JanOrtego Martínez, María IsabelPawlowsky Glahn, VeraMeasurements in sequencing studies are mostly based on counts. There is a lack of theoretical developments for the analysis and modelling of this type of data. Some thoughts in this direction are presented, which might serve as a seed. The main issues addressed are the compositional character of multinomial probabilities and the corresponding representation in orthogonal (isometric) coordinates, and modelling distributions for sequencing data taking into account possible effects of amplification techniques.Some inequalities involving convergent series
http://hdl.handle.net/2117/336852
Some inequalities involving convergent series
Díaz Barrero, José Luis
In this short note Carleman's inequality is combined with convergent series to obtain new inequalities.
Thu, 04 Feb 2021 08:25:04 GMThttp://hdl.handle.net/2117/3368522021-02-04T08:25:04ZDíaz Barrero, José LuisIn this short note Carleman's inequality is combined with convergent series to obtain new inequalities.Sum of cubes of Pellian numbers: OQ5399
http://hdl.handle.net/2117/336851
Sum of cubes of Pellian numbers: OQ5399
Díaz Barrero, José Luis
Thu, 04 Feb 2021 08:21:42 GMThttp://hdl.handle.net/2117/3368512021-02-04T08:21:42ZDíaz Barrero, José LuisThe last three decades of Lalescu limit
http://hdl.handle.net/2117/336648
The last three decades of Lalescu limit
Batinetu Giurgiu, Dumitru; Stanciu, Neculai; Díaz Barrero, José Luis
This article presents alternative solutions to some problems involving Lalescu’s sequence that have been published in problem magazines around the world.
Tue, 02 Feb 2021 10:33:28 GMThttp://hdl.handle.net/2117/3366482021-02-02T10:33:28ZBatinetu Giurgiu, DumitruStanciu, NeculaiDíaz Barrero, José LuisThis article presents alternative solutions to some problems involving Lalescu’s sequence that have been published in problem magazines around the world.A new bound for the moduli of the zeros
http://hdl.handle.net/2117/336647
A new bound for the moduli of the zeros
Díaz Barrero, José Luis
In this note, we give an explicit bound for the modules of the zeros of a polynomial that involves binomial coefficients and recursive numbers.
Tue, 02 Feb 2021 10:31:06 GMThttp://hdl.handle.net/2117/3366472021-02-02T10:31:06ZDíaz Barrero, José LuisIn this note, we give an explicit bound for the modules of the zeros of a polynomial that involves binomial coefficients and recursive numbers.Seventeen camels problem
http://hdl.handle.net/2117/336644
Seventeen camels problem
Rivero Salgado, Óscar; Díaz Barrero, José Luis
Tue, 02 Feb 2021 10:29:38 GMThttp://hdl.handle.net/2117/3366442021-02-02T10:29:38ZRivero Salgado, ÓscarDíaz Barrero, José LuisAn upper bound for the standard deviation of a random variable
http://hdl.handle.net/2117/336643
An upper bound for the standard deviation of a random variable
Díaz Barrero, José Luis
Tue, 02 Feb 2021 10:27:35 GMThttp://hdl.handle.net/2117/3366432021-02-02T10:27:35ZDíaz Barrero, José Luis