Root tfile overwrite a file

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Root tfile overwrite a file

All commands involve typing plink at the command prompt e.

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All results are written to files with various extensions. The name of the file is by default plink. Often these files will be large: The majority of output files are in a standard plain text 'rectangular' format, with one header row and a fixed number of columns per line.

root tfile overwrite a file

Open up a command prompt or terminal window and perform all analyses by typing commands as described below. When PLINK starts it will attempt to contact the web, to check whether there is a more up-to-date version available or not.

This option can be disabled with the --noweb option on the command line.

When using PLINK on a machine with no, or a very slow, web connection, it may be desirable to turn this feature off. This feature is turned on by default so that users are aware of new versions that may contain important new features or bug fixes. If your current version of PLINK is out of date, then a warning message will be displayed, suggesting that you download and install the current version.

This is the only reason the web connection is made -- no other data is transmitted to the server. If the current version is up-to-date, you will see something like the following: Web-based version check --noweb to skip Connecting to web If new commands are added to the command line, they will also be included; if the command also appeared in the original file, any parameters will be taken from the newer version.

For example, if the original command was plink --file mydata --pheno pheno. Note that commands in the old LOG file can be overwritten but not removed with the rerun command.

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Note By default, the --out statement would also be copied, and so the new output would overwrite any old results i. It is often a good idea to also add a new --out command, therefore: In this case, use the --script option, where the remaining options will be read from a text file.

For example, plink --script myscript1. Another advantage of using script files is that it aids attempts at making one's research reproducible. As well as the --file command described above, PED and MAP files can be specified separately, if they have different names: PLINK will give an error message in most circumstances when something has gone wrong.

The PED file is a white-space space or tab delimited file: A PED file must have 1 and only 1 phenotype in the sixth column. The phenotype can be either a quantitative trait or an affection status column: PLINK will automatically detect which type i. However, these individuals will be dropped from any analyses i.

root tfile overwrite a file

HINT To disable the automatic setting of the phenotype to missing if the individual has an ambiguous sex code, add the --allow-no-sex option.

When using a data generation command e. This behaviour can be changed by adding the flag --must-have-sex. The rest of that line will be ignored. Do not start any family IDs with this character therefore.

Affection status, by default, should be coded: It can be reset by including the --missing-phenotype option:/* strex standard styling */.strex-container,feelthefish.com-reveal,.strex-all { position:relative; }.strex-open,.strex-start,.strex-end { color.

This TiddlyWiki contains the following tiddlers: $:/config/DefaultSidebarTab $:/core $:/DefaultTiddlers $:/Import $:/isEncrypted $:/SiteSubtitle $:/SiteTitle $:/state. sfattr is a useful diagnostic program.

It reports certain statistical values for an RSF dataset: RMS (root-mean-square) amplitude, mean value, vector norm value, variance, standard deviation, maximum and minimum values, number of nonzero samples, and the total number of samples. sfattr is a useful diagnostic program.

It reports certain statistical values for an RSF dataset: RMS (root-mean-square) amplitude, mean value, vector norm value, variance, standard deviation, maximum and minimum values, number of nonzero samples, and the total number of samples.

This TiddlyWiki contains the following tiddlers: $:/config/DefaultSidebarTab $:/core $:/DefaultTiddlers $:/Import $:/isEncrypted $:/SiteSubtitle $:/SiteTitle $:/state. This TiddlyWiki contains the following tiddlers: /Users/pete/src/feelthefish.com $:/config/DefaultSidebarTab $:/config/Navigation.

PLINK: Whole genome data analysis toolset