PLINK help Post: 302694815

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Top Forums Shell Programming and Scripting PLINK help Post 302694815 by smitra on Friday 31st of August 2012 12:24:59 PM

08-31-2012

Registered User

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:

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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LEARN ABOUT OPENSOLARIS

mlib_videocoloryuv444int_to_argbint

mlib_VideoColorYUV444int_to_ARGBint(3MLIB)		    mediaLib Library Functions			mlib_VideoColorYUV444int_to_ARGBint(3MLIB)

NAME

       mlib_VideoColorYUV444int_to_ARGBint - color convert YUV interleaved to ARGB interleaved

SYNOPSIS

       cc [ flag... ] file... -lmlib [ library... ]
       #include <mlib.h>

       void mlib_VideoColorYUV444int_to_ARGBint(mlib_u32 *ARGB,
	    const mlib_u8 *YUV, const mlib_u8 *A_array, mlib_u8 A_const,
	    mlib_s32 w, mlib_s32 h, mlib_s32 dlb,
	    mlib_s32 slb, mlib_s32 alb);

DESCRIPTION

       The  YUV pixel stream is converted into an ARGB pixel stream. All pixel components are 8-bit unsigned integers. All buffers have dimensions
       w and h.

       The alpha values for this function work in the following fashion:

	   o	  If A_array pointer is not NULL, the values are taken from there. It has to have the same dimensions as the Y buffer.

	   o	  If A_array pointer is NULL, the alpha values for every pixel are set to A_const.

       The following equation is used:

	 |R|   |1.1644	0.0000	1.5966|   [|Y|	 | 16.0000|]
	 |G| = |1.1644 -0.3920 -0.8132| * [|U| - |128.0000|]
	 |B|   |1.1644	2.0184	0.0000|   [|V|	 |128.0000|]

PARAMETERS

       The function takes the following arguments:

       ARGB	  Pointer to output buffer.

       YUV	  Pointer to Y input buffer.

       A_array	  Array of alpha values.

       A_const	  Constant alpha value.

       w	  Image width in pixels.

       h	  Image height in lines.

       dlb	  Linebytes for output buffer.

       slb	  Linebytes for input buffer.

       alb	  Linebytes for alpha buffer.

RETURN VALUES

       None.

ATTRIBUTES

       See attributes(5) for descriptions of the following attributes:

       +-----------------------------+-----------------------------+
       |      ATTRIBUTE TYPE	     |	    ATTRIBUTE VALUE	   |
       +-----------------------------+-----------------------------+
       |Interface Stability	     |Committed 		   |
       +-----------------------------+-----------------------------+
       |MT-Level		     |MT-Safe			   |
       +-----------------------------+-----------------------------+

SEE ALSO

       mlib_VideoColorYUV420seq_to_ARGBint(3MLIB),     mlib_VideoColorYUV411seq_to_ARGBint(3MLIB),     mlib_VideoColorYUV422seq_to_ARGBint(3MLIB),
       mlib_VideoColorYUV444seq_to_ARGBint(3MLIB),     mlib_VideoColorYUV420seq_to_ABGRint(3MLIB),     mlib_VideoColorYUV411seq_to_ABGRint(3MLIB),
       mlib_VideoColorYUV422seq_to_ABGRint(3MLIB),    mlib_VideoColorYUV444seq_to_ABGRint(3MLIB),     mlib_VideoColorYUYV422int_to_ARGBint(3MLIB),
       mlib_VideoColorYUYV422int_to_ABGRint(3MLIB),    mlib_VideoColorYUV444int_to_ABGRint(3MLIB),    mlib_VideoColorUYVY422int_to_ARGBint(3MLIB),
       mlib_VideoColorUYVY422int_to_ABGRint(3MLIB),    mlib_VideoColorUYV444int_to_ARGBint(3MLIB),     mlib_VideoColorUYV444int_to_ABGRint(3MLIB),
       attributes(5)

SunOS 5.11							    2 Mar 2007				mlib_VideoColorYUV444int_to_ARGBint(3MLIB)

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