PLINK: Whole genome data analysis toolset
PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data).
PLINK: Whole genome data analysis toolset
When creating a binary ped file, the MAF and missingness filters are set to include everybody and all SNPs. If you want to change these, use –maf, –geno, etc, to manually specify these options: for example, plink –file mydata –make-bed –maf 0.02 –geno 0.1
Standard data input
For example, plink –bfile toy–bed bob–freq would reference the binary fileset bob.bed + toy.bim + toy.fam. (.fam files are also present in some other fileset types. The –fam flag has the same function when loading them.)–keep-autoconv PLINK 1 binary is PLINK
10 PuTTY PLINK Examples to Automate Remote Linux …
In the following example, plink will connect to the remote Linux server on port 25. C:\>plink [email protected] -P 25 crontab -l When you use a saved PuTTY session and -P option, instead of using the port from the saved session, it will use the given Port.
Data management Generate binary fileset–make-bed–make-bed creates a new PLINK 1 binary fileset, after applying sample/variant filters and other operations below. For example, plink –file text_fileset–maf 0.05–make-bed –out binary_fileset does the following:
Limiting Reagents Practice Problems
Practice Problems: Limiting Reagents Take the reaction: NH 3 + O 2 NO + H 2 O. In an experiment, 3.25 g of NH 3 are allowed to react with 3.50 g of O 2. Hint a. Which reactant is the limiting reagent? b. How many grams of NO are formed? c. How much of the
Chapter 7: Using the command-line connection tool …
For example, plink login.example.com -l fred. Set up a PuTTY saved session that describes the server you are connecting to, and that also specifies the username to log in as (see section 4.14.1 ). To avoid being prompted for a password, you should almost certainly set up public-key authentication.
$ plink –bfile mydata –linear # traits 是數字 $ plink –bfile mydaya –logistic # traits 是字母 $ head plink.assoc.logistic CHR SNP BP A1 TEST NMISS OR STAT P 1 rs3094315 792429 G ADD 89 2 連鎖不平衡反應 chapter 13
Example: Human leukocyte antigen (HLA) alleles HLA constitutes a group of cell surface antigens also known as the MHC of humans. Because HLA genes are located at adjacent loci on the particular region of a chromosome and presumed to exhibit epistasis with each other or with other genes, a sizable fraction of alleles are in linkage disequilibrium.
For example, for the 0.05 threshold, we include all SNPs with P-value from 0 to 0.05, including any SNPs with P-value equal to 0.05. We can then calculate the PRS with the following plink command: plink \ –bfile EUR.QC \ –score Height.QC.Transformed 3 4 12 header \ –q-score-range range_list SNP.pvalue \ –extract EUR.valid.snp \ –out EUR
生信分析預處理，沒關系 4.第四列是物理距離 5.第五列是次要等位基因 6.第六
Can we add additional columns to ped and map files in …
· Hello, I need to know whether we can add additional columns to PLINK file formats. Specifically, I am trying to create PLINK file formats, by using my simulated data. I need to know that in a .ped file format in PLINK, can we add additional columns (ex: a column
· Example input: 3000 3001 3002 Command: python liftRsNumber.py input.rs > output.rs Example output: unchanged 3000 lifted 2032 unchanged 3002 Lift Merlin/PLINK format In Merlin/PLINK .map files, each line contains both genome position and dbSNP
Download PuTTY: latest release (0.74)
32-bit Arm: plink.exe 32-bit Arm: pageant.exe 32-bit Arm: puttygen.exe Zip file of all Windows on Arm executables 64-bit Arm: putty.zip 32-bit Arm: putty.zip Checksum files Cryptographic checksums for all the above files MD5: md5sums SHA-1: sha1sums
Laplink PCmover is PC migration software developed by Laplink Software.Introduced in 2005, as the successor to Laplink, PCmover comes in a variety of versions that provide the ability to move or restore all selected files, folders, settings, user profiles and programs from an old PC to a new one, an old operating system to a new one, or an old hard drive to a new one.
For example: 1055678912345 Online check-in opens 36 hours before departure, or 24 hours before departure for flights to/from the USA. If you are denied boarding or if your flight is cancelled or delayed for at least two hours, ask at the check-in counter or boarding gate for the text stating your rights, particularly with regard to compensation and assistance.
PCmover Business – Small & Medium Business Migration …
EXAMPLE: Let’s say you purchase a 10-Use Technician License on the 27th day of a month, and only use 4 before the month ends. You only pay for those 4, and your count goes back up …
，代表的數據意義和其他兩個文件對應， bed bed文件采用二進制的方式保存文件，plink兩種格式識別與轉換 文件格式1 bed fam bim 是一組的， bim 1.第一列是染色體信息 2.第二列是snp的名字 3.第三列是摩爾距離