Shulou(Shulou.com)06/01 Report--

This article is to share with you about the plink PED file format, the editor thinks it is very practical, so I share it with you to learn. I hope you can get something after reading this article.

Plink is one of the commonly used software for genome-wide association analysis, which requires two basic formats of input files, ped and map. This article focuses on the ped format.

For ped format, it contains the following information

Family structure

Gender information

Phenotypic information

Snp calling information

The ped format is a plain text file that requires at least 6 columns, each with spaces or\ t delimited. These six columns

Respectively represent the following meanings

Family ID

Individual ID

Paternal ID

Maternal ID

Sex

Phenotype

Family ID is used to represent the family, the same family is represented by the same family ID; Individual ID is used to represent the individual, family ID and Individual ID must be connected to represent each sample uniquely; Paternal ID represents the male parent ID, Maternal ID represents the female parent ID, through the above four attributes, the family structure information of the sample can be completely represented.

Sex stands for gender, 1 for male,2 for female, and other numbers for unknown.

Phenotype represents the phenotype, where the phenotype can be discrete (such as qualitative traits) or continuous (such as quantitative traits), and plink will automatically identify the corresponding types. Through the above six necessary fields, it can be completely mapped to the family map of a certain character.

For association analysis, genotypic information is needed in addition to phenotypic information. In a file in ped format, the remaining columns are usually used to represent genotype information. In the ped file, the genotype of each snp locus needs to be represented by two columns, which represent major allel and minor allel respectively. In the expression of genotypes, we can use either the form of the letter AMagre C, or the form of numeric coding, which is called "1" and "2". By default, 0 is used to indicate the deletion of the genotype.

An example of an ped file is as follows

1 1 0 0 1 1 An A G T2 1 0 0 1 1 A C T G3 1 0 0 1 1 C C G G4 1 0 0 1 2 A C T T5 1 0 0 1 2 C C G T6 1 0 0 1 2 C C T T

In this ped file, all samples are independent of each other, there is no genetic relationship, so each sample has a unique family ID; for the sample, only need the information of family ID and Individual ID fields to connect, can only represent a sample, because family ID and the sample is an one-to-one correspondence, so the Individual ID here is unified with 1.

Because there is no genetic relationship, Paternal ID and Maternal ID are meaningless, the values of all are 0; the sex is all 1, indicating that all samples are male; the values of phenotype are 1 and 2, which are discrete. The last four columns of information represent the genotypic information of two SNP loci, one SNP locus for every two columns.

The above is what the plink PED file format is, and the editor believes that there are some knowledge points that we may see or use in our daily work. I hope you can learn more from this article. For more details, please follow the industry information channel.

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