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Full Discussion: PLINK help
Top Forums Shell Programming and Scripting PLINK help Post 302694815 by smitra on Friday 31st of August 2012 12:24:59 PM
Old 08-31-2012
Thanks Corona688,
My file format is like:
Code:
Sample Name	SNP Name	Sample ID	Allele1 - Top	Allele2 - Top	GC Score	Allele1 - Forward	Allele2 - Forward	Allele1 - Design	Allele2 - Design	Allele1 - AB	Allele2 - AB	Allele1 - Plus	Allele2 - Plus	Chr	Position	GT Score	Cluster Sep	SNP	ILMN Strand	Customer Strand	Top Genomic Sequence	Plus/Minus Strand	Theta	R	X	Y	X Raw	Y Raw	B Allele Freq	Log R Ratio	CNV Value	CNV Confidence
	200610-104	P001	A	A	0.4097	T	T	T	T	A	A	T	T	MT	212	0.8207	1.0000	[T/C]	BOT	BOT		+	0.010	2.315	2.281	0.034	35825	464	0.0042	-0.1955		
	200610-106	P001	A	A	0.2638	T	T	A	A	A	A	A	A	MT	246	0.7865	1.0000	[A/G]	TOP	BOT		+	0.106	2.202	1.884	0.318	29655	3030	0.0661	-0.3255		
	200610-119	P001	A	A	0.3616	T	T	T	T	A	A	T	T	MT	5049	0.7771	1.0000	[T/C]	BOT	BOT		+	0.035	2.515	2.382	0.133	37410	1369	0.0000	-0.0959		
	200610-137	P001	A	A	0.3616	T	T	T	T	A	A	T	T	MT	12286	0.7771	1.0000	[T/C]	BOT	BOT		+	0.086

Now obviously for Plink (Whole genome data analysis toolset....which is a comandline program for GWAS ) I don't need all the columns. So I managed to create bim and fam files using awk. But now I need binary bed file (which is not liek usual .bed files). That is why I was looking for any user who used PLINK before.

I think there are some option like --make-bed supplying bim and fam files; but I am not sure if I am doing it right.

Any help will be really great Smilie
Thanks a lot,
Mitra

Moderator's Comments:
Mod Comment edit by bakunin: Please use code tags next time for your code and data.

Last edited by bakunin; 09-01-2012 at 07:01 PM..
 

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ICONV_MIME_DECODE_HEADERS(3)						 1					      ICONV_MIME_DECODE_HEADERS(3)

iconv_mime_decode_headers - Decodes multiple MIMEheader fields at once

SYNOPSIS
array iconv_mime_decode_headers (string $encoded_headers, [int $mode], [string $charset = ini_get("iconv.internal_encoding")]) DESCRIPTION
Decodes multiple MIME header fields at once. PARAMETERS
o $encoded_headers - The encoded headers, as a string. o $mode -$mode determines the behaviour in the event iconv_mime_decode_headers(3) encounters a malformed MIME header field. You can spec- ify any combination of the following bitmasks. Bitmasks acceptable to iconv_mime_decode_headers(3) +------+--------------------------------------+---+ |Value | | | | | | | | | Constant | | | | | | | | Description | | | | | | +------+--------------------------------------+---+ | 1 | | | | | | | | | ICONV_MIME_DECODE_STRICT | | | | | | | | If set, the given header is decoded | | | | in full conformance with the stan- | | | | dards defined in RFC2047. This | | | | option is disabled by default | | | | because there are a lot of broken | | | | mail user agents that don't follow | | | | the specification and don't produce | | | | correct MIME headers. | | | | | | | 2 | | | | | | | | | ICONV_MIME_DECODE_CONTINUE_ON_ERROR | | | | | | | | If set, iconv_mime_decode_head- | | | | ers(3) attempts to ignore any gram- | | | | matical errors and continue to | | | | process a given header. | | | | | | +------+--------------------------------------+---+ o $charset - The optional $charset parameter specifies the character set to represent the result by. If omitted, iconv.internal_encoding will be used. RETURN VALUES
Returns an associative array that holds a whole set of MIME header fields specified by $encoded_headers on success, or FALSE if an error occurs during the decoding. Each key of the return value represents an individual field name and the corresponding element represents a field value. If more than one field of the same name are present, iconv_mime_decode_headers(3) automatically incorporates them into a numerically indexed array in the order of occurrence. EXAMPLES
Example #1 iconv_mime_decode_headers(3) example <?php $headers_string = <<<EOF Subject: =?UTF-8?B?UHLDvGZ1bmcgUHLDvGZ1bmc=?= To: example@example.com Date: Thu, 1 Jan 1970 00:00:00 +0000 Message-Id: <example@example.com> Received: from localhost (localhost [127.0.0.1]) by localhost with SMTP id example for <example@example.com>; Thu, 1 Jan 1970 00:00:00 +0000 (UTC) (envelope-from example-return-0000-example=example.com@example.com) Received: (qmail 0 invoked by uid 65534); 1 Thu 2003 00:00:00 +0000 EOF; $headers = iconv_mime_decode_headers($headers_string, 0, "ISO-8859-1"); print_r($headers); ?> The above example will output: Array ( [Subject] => Prufung Prufung [To] => example@example.com [Date] => Thu, 1 Jan 1970 00:00:00 +0000 [Message-Id] => <example@example.com> [Received] => Array ( [0] => from localhost (localhost [127.0.0.1]) by localhost with SMTP id example for <example@example.com>; Thu, 1 Jan 1970 00:00:00 +0000 (UTC) (envelope-from example-return-0000-example=example.com@example.com) [1] => (qmail 0 invoked by uid 65534); 1 Thu 2003 00:00:00 +0000 ) ) SEE ALSO
iconv_mime_decode(3), mb_decode_mimeheader(3), imap_mime_header_decode(3), imap_base64(3), imap_qprint(3). PHP Documentation Group ICONV_MIME_DECODE_HEADERS(3)
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