File format reference PLINK 1. Introduction, downloads. S 1. 4 Nov 2. 01. D 4 Dec 2. 01. 7Recent version history. Whats. new Future development. Limitations. Note to testersJump to search boxGeneral usage. Citation instructions. Standard data input. PLINK 1 binary. Autoconversion behavior. PLINK text. ped,. VCF. vcf. gz,. Oxford. Me text. Generate random. Unusual chromosome IDs. Recombination map. Phenotypes. Covariates. Clusters of samples. Fa0f%2Fa0f57d20-ce53-43ce-b6de-12ee81e286c4%2FphpiA1NPz.png' alt='Plot Data From Mat File' title='Plot Data From Mat File' />MATLAB Commands 5 InputOutput and Formatting Commands InputOutput Commands disp Displays contents of an array or string. Read formatted data from a file. PO/so_globec/surface_17_1_all_topo30_1min.jpg' alt='Plot Data From Mat File' title='Plot Data From Mat File' />Variant sets. Binary distance matrix. IBD report. genomeInput filtering. Sample ID file. Variant ID file. Positional ranges file. Cluster membership. Set membership. Attribute based. Chromosomes. SNPs only. Data Files In the database of the website you will find thousands of popular as well as rare file extensions, and the thousands of programs that can be used to. Simple variant window. Multiple variant ranges. Samplevariant thinning. Covariates filterMissing genotypes. Missing phenotypes. Minor allele frequencies. Hardy Weinberg. Mendel errors. Quality scores. Relationships. Main functions. Data management make bed recode output chr zero cluster split x merge x set me missing fill missing a. Merge failures. VCF reference merge merge list write snplist list duplicate vars. Basic statistics freqx missing test mishap hardy mendel het ibc check sex impute sex fst. Linkage disequilibrium indep. Distance matrices. Identity by stateHamming  distance. Relationshipcovariance  make grm bin. Distance pheno. analysis  ibs test. Identity by descent genome homozyg. Population stratification cluster pca mds plot neighbour. Association analysis. Basic casecontrol  assoc, modelStratified casecontrol  mh, mh. Quantitative trait  assoc, gxeRegression w covariates  linear, logistic dosage lasso test missing. Monte Carlo permutation. Set based tests. REML additive heritability. Family based association tdt dfam qfam. Report postprocessing annotate clump gene report meta analysis. Epistasis fast epistasis epistasis twolocus. Allelic scoring scoreR plugins RSecondary input. GCTA matrix. grm. Distributed computation. Command line help. Miscellaneous. Tabs vs. Flagparameter reuse. System resource usage. Pseudorandom numbers. Resources. 10. 00 Genomes phase 1. Teaching materials. Gene range lists. Functional SNP attributes. Errors and warnings. Output file list. Order of operations. For developers. Git. Hub repository. Compilation. Core algorithms. Partial sum lookup. Bit population count. Ternary dot product. Vertical population count. Exact statistical tests. Multithreaded g Adding new functionality. Google groupsplink. Credits. File formats. Quick index search. This page describes specialized PLINK input and output file formats which are. Most extensions not listed here have very. Jump to. adjusted. N. bin. hom. indiv. Produced by adjust. A text file with a header line, and then one line per set or polymorphic. CHRChromosome code. Not present with set. SNPSETVariantset identifier. UNADJUnadjusted p value. GCDevlin Roeder 1. Requires an additive model. QQP value quantile. Only present with qq plot. BONFBonferroni correction. HOLMHolm Bonferroni 1. SIDAKSSidk single step adjusted. SIDAKSDidk step down adjusted. FDRBHBenjamini Hochberg 1. FDRBYBenjamini Yekutieli 2. Variantssets are sorted in p value order. As a result, if the QQ field. Produced by update alleles when there is a mismatch between the loaded alleles. A text file with no header line, and one line per mismatching variant with. Variant identifier. Expected allele 1 from update alleles input fileExpected allele 2 casecontrol association. Produced by assoc acting. A text file with a header line, and then one line per variant typically. CHRChromosome code. SNPVariant identifier. BPBase pair coordinate. A1. Allele 1 usually minorFAAllele 1 frequency among cases. FUAllele 1 frequency among controls. A2. Allele 2. CHISQAllelic test chi square statistic. Not. present with fisherfisher midp modifier. PAllelic test p value. ORoddsallele 1 case oddsallele 1 controlIf the counts modifier is present, the 5th and 6th fields are replaced. CAAllele 1 count among cases. CUAllele 1 count among controls. If ci 0. xy has also. SEStandard error of odds ratio estimate. Lxy. Bottom of xy symmetric approx. Hxy. Top of xy approx. Produced by dosage. A text file with a header line, and then usually one line per variant with. CHRChromosome code. Requires map. SNPVariant identifier. BPBase pair coordinate. Requires map. A1. Allele 1 usually minorA2. Allele 2 usually majorFRQAllele 1 frequency. INFOR squared quality metricinformation contentBETAORRegression coefficient for quantitative. Torrent Sean Paul Full Frequency Song there. SEStandard error of effect not odds ratio estimate. PAssociation test p value. If the case control freqs modifier is present, the FRQ column is. FRQA and FRQU columns reporting case and control. NCHROBS will not include missing phenotype. Unless the phenotype is quantitative instead of casecontrol. FRQA and FRQU are both equal to the. FRQ value. Produced by linear logistic. A text file with a header line, and T lines per variant typically. T is normally the number of. CHRChromosome code. Not present with no snp. SNPVariant identifier. Not present with. BPBase pair coordinate. Not present with. A1. Allele 1 usually minor. Not present with. TESTTest identifier. NMISSNumber of observations nonmissing genotype. BETAORRegression coefficient linear, logistic. STATT statistic. PAsymptotic p value for t statistic. If ci 0. xy has also been specified, the following three fields. STAT SEStandard error of betaodds ratio estimate. Lxy. Bottom of xy symmetric approx. Hxy. Top of xy approx. Refer to the PLINK 1. Produced by R. A text file with no header line, and one line per variant, each with at. The first four are Chromosome code. Variant identifier. Base pair coordinate. Allele 1 corresponding to allele counts in GENO matrix usually. Subsequent fields are defined by the plugin function. Lines are permitted. Variant information sample ID genotype call binary file, loaded with. Cannot currently be generated by PLINK use. VCF file for now. The specification for this format is at http www. Produced by recode. BEAGLE. In beagle mode, one file pair is generated per autosome, while in. This format cannot be loaded by. PLINK. Each. dat file produced by PLINK is a text file with three header lines. N2 fields where N is. Subsequent contentsPIA for CC pheno., T for scalarMFIDIIDPHEVariant identifier. FIDs, 2x per sample. IIDs, 2x per sample. Phenotypes, 2x per sample. Allele calls unphasedEach. PLINK is a text file with no header line. Variant identifier. Base pair coordinate. Allele 1 usually minor, X if absent. Allele 2 usually major, X if absent. Primary representation of genotype calls at biallelic variants. Must be. accompanied by. Loaded with bfile generated. Do not confuse this with the UCSC Genome. Browsers BED format, which is totally different. The first three bytes should be 0x. There are old versions of the. PLINK 1. 9 recognizes them, but will convert. See the. bottom of the original. The rest of the file is a sequence of V blocks of. N4 rounded up bytes each, where V is the number of. N is the number of samples. The first block. corresponds to the first marker in the. The low order two bits of a blocks first byte store the first. First sample here means the first sample listed. Matched Wikipedia. Matched, by Allyson Braithwaite Condie, is the first novel in the Matched trilogy. The novel is a dystopian young adult novel about a tightly controlled society in which young people are matched with their life partners at the age of 1. The main character is seventeen year old Cassia Reyes, who has blood type A and is Matched with her best friend, Xander Carrow. However, when viewing the information for her Match, the picture of another young man Ky Markham, an acquaintance outcast at her school is flashed across the screen. As Cassia attempts to figure out the source of the mishap, she finds herself conflicted about whether her Match is appropriate for her and whether the Society is all that it seems to be. This book is followed by Crossed and Reached. Seventeen year old Cassia Reyes who who has blood type A lives in a futuristic, seemingly utopian Society in which the citizens lives are strictly controlled by the government the government decides where they live, where they work, who they care about and even when they die all citizens die at the age of 8. At the age of seventeen, citizens undergo the process of being matched becoming paired up with another boygirl selected by the authorities. Typically, young men and women are Matched with someone from another town, sometimes even another province they generally do not know their Match ahead of time, but are shown their face over a television screen and subsequently provided with a picture and information about the match on a microcard a piece of storage similar to a floppy disk or flash drive. Matched couples are given a period of courtship, and are then married when they turn 2. The system was devised to give couples their best chance at having healthy children. In return, citizens of the Society live longer and better than any other citizens in the history of the world. At the beginning of the novel, Cassia is led to the Match Banquet by her parents, an elaborate event that happens across her country in different towns at the same time. When Cassias name is called at the Banquet, the TV screen stays dark which means that her Match is somewhere in the same room, from her own town of Mapletree Borough, which rarely happens. She becomes overjoyed when she realizes that her Match is her best friend, Xander Carrow, who goes to her Second School high school and grew up on the same street as she. Cassia is excited about their future together, although her excitement is tempered a bit by disappointment that she already knows everything about Xander and will not have the exciting experience of meeting him for the first time. As the novel progresses, the Society is increasingly portrayed as dystopian. Families are provided with tasteless rationed food, controlled for calories and nutrition there is strict population control, and every family has a port in their household a two way television that allows the government to monitor their behavior, as well as for them to respond to government questions. The ports are also how people read microcards with stored information on them. All people are revealed to have to die on their 8. Society slowly starts to poison the seniors food when they are reaching the end of their 7. The Society has also decided that their former culture was too cluttered and thus eliminated most traces of culture, saving only 1. Hundred Poems, Hundred Paintings, Hundred Stories, Hundred Songs, etc. At night, citizens take turn with their family members wearing data tags, which collect information on their dreams to help predict their behavior. Every citizen must also carry three pills on them one blue, one green, and one red although initially it is not revealed what the tablets do. Cassia carries her pills in an artifact a possession from the past that was given to her by her grandfather that used to be a powder compact used by her great grandmother. Peoples actions are predicted using sophisticated psychological and statistical techniques, referred to as sorting. Cassias assigned adult job is as a sorter, and she is noted to be gifted at this particular job. Cassia enjoys it, but notes that she does not want to sort real people such as sorting them into jobs or Matches. After school and practicing her trade, Cassia returns home and decides to view the information about Xander on her microcard on the port. When she inserts the microcard, Xanders face pops up, but then the screen glitches and displays another face that of Ky Markham, another young man who lives in her borough. Ky is an aberration, which is a person who has been revoked of citizen status. Ky was adopted by his aunt and uncle, Aida and Patrick Markham, after their own son was killed by a dangerous Anomaly, an outcast member of society. Ky is good looking, but he is very quiet and keeps to himself, having left school early to accept his work assignment at the nutrition disposal center, a notoriously difficult job. The Official confides in Cassia that Ky is not meant to be Matched with anyone, as he is an Aberration a semi outcast member of society who usually acquires this identity through committing an Infraction. A Society Official tells Cassia that Kys father committed a serious Infraction, and although Ky was allowed to be adopted by his aunt and uncle at a young age, he had to retain his identity as an Aberration and therefore cannot be Matched with anyone. Cassia only tells her beloved grandfather, a man nearing his 8. Her grandfather encourages her to find the words within her and gives her a forbidden piece of paper. Cassia has chosen hiking as her summer recreation activity, and while in the woods she peeks at her grandfathers paper. On it are two poems that are not in the Societys allotted Hundred Poems, a dangerous infraction. Coincidentally, Ky Markham has also chosen hiking, and he spots her in the woods reading the paper. He promises to keep her secret and help her destroy the poems after she memorizes them. As he helps her first destroy the poems then preserve the memory of them and teaches her how to write words in the dirt Cassia slowly falls in love with Ky, and he with her. Her growing feelings for Ky make her question her relationship with Xander and the wisdom of the Matching system over time, she grows more and more frustrated with the Societys control over her relationship and her ability to express herself through poetry and writing, which is forbidden. Gradually, Cassia begins to discover that the Society is not as utopian as she had once thought in that peoples freedoms are severely restricted, and the people are not allowed to make choices about their own desires and wants including who they want to spend their lives with and whether they would like to be preserved for science at all. Cassia struggles with her inner desire to rebel and her more overt desire to remain docile, give into the Society and allow it to take care of her basic needs in return for a loss of freedom. It is also gradually revealed what the three tablets do the green is a sort of sedative that calms people when they have anxiety. The blue tablet is described as providing nourishment for people who may be separated from food for a long time. And the red tablet causes people to forget anything that has happened in the last 1. Xander and Ky. The Officials take all the artifacts because they are considered Unequal.