Input files - Revision history

127.0.0.1: /* Allele frequency file */

2022-08-31T23:42:36Z

Allele frequency file

← Older revision		Revision as of 23:42, 31 August 2022
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	A file containing allele frequencies must be in block format and contain a single block named {{cc\|FREQUENCIES}}.		A file containing allele frequencies must be in block format and contain a single block named {{cc\|FREQUENCIES}}.
	As an example, for 10 markers the file content is		As an example, for 5 markers and setting the allele frequencies to 0.5 the file content is


			BEGIN FREQUENCIES
			real,array,64,10
			1.0
			1.0
			1.0
			1.0
			1.0
			END FREQUENCIES

	Note that the allele frequencies must be expressed as expected allele content(2p).		Note that the allele frequencies must be expressed as expected allele content(2p).
	~~As an example, setting all allele frequencies to 0.5~~ can be ~~achieved by generating a pq file~~ in R		A pqfile can be generated in R by

	<syntaxhighlight lang="R" line>		<syntaxhighlight lang="R" line>

127.0.0.1: /* Allele frequency file */

2022-08-31T23:40:22Z

Allele frequency file

← Older revision		Revision as of 23:40, 31 August 2022
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	== Allele frequency file ==		== Allele frequency file ==

	A file containing allele frequencies must be in block format and contain a single block named {{cc\|FREQUENCIES}}. Note that the allele frequencies must be expressed as expected allele content(2p).		A file containing allele frequencies must be in block format and contain a single block named {{cc\|FREQUENCIES}}.
			As an example, for 10 markers the file content is


			Note that the allele frequencies must be expressed as expected allele content(2p).
	As an example, setting all allele frequencies to 0.5 can be achieved by generating a pq file in R		As an example, setting all allele frequencies to 0.5 can be achieved by generating a pq file in R

127.0.0.1: /* Allele frequency file */

2022-08-31T23:37:45Z

Allele frequency file

← Older revision		Revision as of 23:37, 31 August 2022
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	</syntaxhighlight>		</syntaxhighlight>

	and providing it to {{~~cc\|LMT~~}}.		and providing it to {{lmt}}.

127.0.0.1: /* Allele frequency file */

2022-08-31T23:37:14Z

Allele frequency file

← Older revision		Revision as of 23:37, 31 August 2022
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	A file containing allele frequencies must be in block format and contain a single block named {{cc\|FREQUENCIES}}. Note that the allele frequencies must be expressed as expected allele content(2p).		A file containing allele frequencies must be in block format and contain a single block named {{cc\|FREQUENCIES}}. Note that the allele frequencies must be expressed as expected allele content(2p).
	As an example, setting all allele frequencies to 0.5 can be achieved by		As an example, setting all allele frequencies to 0.5 can be achieved by generating a pq file in R

			<syntaxhighlight lang="R" line>
			x=list(FREQUENCIES=rep(1,nmarker))
			writelmtblockfile(x,"pq.blkcsv","txt")
			</syntaxhighlight>

			and providing it to {{cc\|LMT}}.

127.0.0.1: /* Genotype file */

2022-08-31T23:35:17Z

Genotype file

← Older revision		Revision as of 23:35, 31 August 2022
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	1211121121111120110001110201111020111111		1211121121111120110001110201111020111111
	Note that additional information about the genotypes, e.g. the pedigree ids of the related individuals, maybe supplied via an additional file.		Note that additional information about the genotypes, e.g. the pedigree ids of the related individuals, maybe supplied via an additional file.

			== Allele frequency file ==

			A file containing allele frequencies must be in block format and contain a single block named {{cc\|FREQUENCIES}}. Note that the allele frequencies must be expressed as expected allele content(2p).
			As an example, setting all allele frequencies to 0.5 can be achieved by

Boerner at 06:30, 4 March 2022

2022-03-04T06:30:38Z

← Older revision		Revision as of 06:30, 4 March 2022
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			lmt '''does not require''' the user to provide information about the file content. Depending on the prospective use lmt will expect a particular file content and will try to read the file accordingly. For example

			*the data file is supposed to contain only real/float numbers which are transferred to integer if required,
			*a file containing an ordinary pedigree is supposed to contain only integer numbers,
			*a file containing a missing value indicator matrix is supposed to contain only character strings, etc.

	== data file ==		== data file ==

Boerner at 05:50, 4 March 2022

2022-03-04T05:50:29Z

← Older revision		Revision as of 05:50, 4 March 2022
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	~~== File content determination via file name extensions ==~~		== data file ==
	~~{{lmt}} automatically detects the format of input files by the [https://en.wikipedia.org/wiki/Filename_extension filename extension]. Supported extensions are~~
	*".csv" for ordinary [https://en.wikipedia.org/wiki/Comma-separated_values comma separated values] ascii text files
	*".blkcsv" for comma separated value ascii text files in block format
	*".bin" for binary files in block format

	~~Note that this mechanism does not apply to files containing genotypes.~~

	~~== ".csv" files ==~~

	~~".csv" files may contain several commented lines at the top only where the comment character is "#".~~

	~~The type of the file content is determined by its prospective use, that is~~
	*the data file is supposed to contain only real/float numbers which are transferred to integer if required,
	*a file containing an ordinary pedigree is supposed to contain only integer numbers,
	*a file containing a missing value indicator matrix is supposed to contain only character strings.

	=== data file ===

	{{lmt}} accepts only a single file containing the actual data. A data file in ".csv" format must follow the following formatting rules:		{{lmt}} accepts only a single file containing the actual data. A data file in ".csv" format must follow the following formatting rules:
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	28.3,1,8		28.3,1,8

	=== co-variance matrix file ===		== co-variance matrix file ==

	A co-variance matrix files must contain a single full squared symmetric positive definite matrix. The content of a co-variance file maybe named "sigma.csv" may look like		A co-variance matrix files must contain a single full squared symmetric positive definite matrix. The content of a co-variance file maybe named "sigma.csv" may look like
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	</syntaxhighlight>		</syntaxhighlight>

	=== co-variance mask files ===		== co-variance mask files ==

	A co-variance mask file communicates to {{lmt}} which co-variances should remain constant when {{lmt}} is used to estimate variances. The mask file must contain characters which can be interpreted as a [https://en.wikipedia.org/wiki/Boolean_data_type boolean data type], and where "T" codes for co-variances which must remain constant and "F" codes for variances which are allowed to float. The mask file must have the same dimensions as the associated co-variance matrix. For instance the above co-variance matrix file maybe accompanied by a mask file containing		A co-variance mask file communicates to {{lmt}} which co-variances should remain constant when {{lmt}} is used to estimate variances. The mask file must contain characters which can be interpreted as a [https://en.wikipedia.org/wiki/Boolean_data_type boolean data type], and where "T" codes for co-variances which must remain constant and "F" codes for variances which are allowed to float. The mask file must have the same dimensions as the associated co-variance matrix. For instance the above co-variance matrix file maybe accompanied by a mask file containing
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	which communicates to {{lmt}} that the first and second diagonal element should remain at their original values.		which communicates to {{lmt}} that the first and second diagonal element should remain at their original values.

	=== missing observations indicator file ===		== missing observations indicator file ==

	The pattern of missing observations maybe communicated via an indicator file, where the file must contain characters which can be interpreted as a [https://en.wikipedia.org/wiki/Boolean_data_type boolean data type], and where "T" codes for an available observation and "F" codes for a missing observation. Further, similar to the data file, the missing value indicator file must contain a header with the same column names as the observation columns in the data file.		The pattern of missing observations maybe communicated via an indicator file, where the file must contain characters which can be interpreted as a [https://en.wikipedia.org/wiki/Boolean_data_type boolean data type], and where "T" codes for an available observation and "F" codes for a missing observation. Further, similar to the data file, the missing value indicator file must contain a header with the same column names as the observation columns in the data file.
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	T,F		T,F

	=== pedigree file ===		== pedigree file ==

	For all types of pedigree described below it is required that		For all types of pedigree described below it is required that
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	It is not necessary that the pedigree is sorted or that a sorting variable(e.g. date of birth) is supplied.		It is not necessary that the pedigree is sorted or that a sorting variable(e.g. date of birth) is supplied.

	==== ordinary pedigree file ====		=== ordinary pedigree file ===
	A file containing an ordinary pedigree must have three numeric columns: individual id,first parent id, second parent id, where the number of unique ids in the first column must be equal to the row dimension of the pedigree.		A file containing an ordinary pedigree must have three numeric columns: individual id,first parent id, second parent id, where the number of unique ids in the first column must be equal to the row dimension of the pedigree.

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	</syntaxhighlight>		</syntaxhighlight>

	==== probabilistic pedigree file ====		=== probabilistic pedigree file ===
	Probabilistic pedigrees account for the possibility that an individual originates from more than one pair of parents. That is, an ordinary pedigree is just a special case of a probabilistic pedigree with all probabilities set to 1. In a probabilistic pedigree individual may have repeated records.		Probabilistic pedigrees account for the possibility that an individual originates from more than one pair of parents. That is, an ordinary pedigree is just a special case of a probabilistic pedigree with all probabilities set to 1. In a probabilistic pedigree individual may have repeated records.
	A file containing an ordinary pedigree must have three numeric columns: individual id,first parent id, second parent id, parentage probability. Within individuals parentage probabilities must sum up to 1. Further, repeated records of the same individual id must be adjacent. For instance		A file containing an ordinary pedigree must have three numeric columns: individual id,first parent id, second parent id, parentage probability. Within individuals parentage probabilities must sum up to 1. Further, repeated records of the same individual id must be adjacent. For instance
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	</syntaxhighlight>		</syntaxhighlight>

	==== genetic group pedigree file ====		=== genetic group pedigree file ===
	Ordinary and probabilistic pedigrees can contain genetic groups. {{lmt}} assumes '''one phantom parent per genetic group''' where the phantom parents must be located at the top of pedigree and must have their parents set to zero. The number of phantom parents is communicated to {{lmt}} as an extra parameter at the appropriate location in the parameter file. Adding phantom parents to a pedigree requires to shift the numbering of the original pedigree by the number of phantom parents. For example the above ordinary pedigree can be transferred into a pedigree with 2 genetic groups, and therefore 2 phantom parents:		Ordinary and probabilistic pedigrees can contain genetic groups. {{lmt}} assumes '''one phantom parent per genetic group''' where the phantom parents must be located at the top of pedigree and must have their parents set to zero. The number of phantom parents is communicated to {{lmt}} as an extra parameter at the appropriate location in the parameter file. Adding phantom parents to a pedigree requires to shift the numbering of the original pedigree by the number of phantom parents. For example the above ordinary pedigree can be transferred into a pedigree with 2 genetic groups, and therefore 2 phantom parents:
	1,0,0		1,0,0
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	</syntaxhighlight>		</syntaxhighlight>

	==== meta-founder pedigree file ====		=== meta-founder pedigree file ===
	The meta-founder concept is very similar to the genetic group concept with the phantom parents becoming meta-founders, and therefore the same format requirements as for the genetic group pedigree apply. The number of meta-founders as well as the meta-founder co-variance matrix are communicated to {{lmt}} as extra parameters at the appropriate location in the parameter file.		The meta-founder concept is very similar to the genetic group concept with the phantom parents becoming meta-founders, and therefore the same format requirements as for the genetic group pedigree apply. The number of meta-founders as well as the meta-founder co-variance matrix are communicated to {{lmt}} as extra parameters at the appropriate location in the parameter file.

	=== Genotype cross-reference file ===		== Genotype cross-reference file ==
	The file contains the pedigree ids of the genotyped individuals as a single column vector. The genotype file and the cross-reference file must have the same number of lines. {{lmt}} will related the individual id and the genotype via the file line number, that is the pedigree id located in line #5 of the cross-reference file is that of an individual of which genotype is located in line #5 of the genotype file.		The file contains the pedigree ids of the genotyped individuals as a single column vector. The genotype file and the cross-reference file must have the same number of lines. {{lmt}} will related the individual id and the genotype via the file line number, that is the pedigree id located in line #5 of the cross-reference file is that of an individual of which genotype is located in line #5 of the genotype file.

Boerner: Boerner moved page Input file formats to Input files

2022-03-04T05:47:03Z

Boerner moved page Input file formats to Input files

← Older revision	Revision as of 05:47, 4 March 2022
(No difference)

Boerner: /* pedigree file */

2021-01-03T06:03:55Z

pedigree file

← Older revision		Revision as of 06:03, 3 January 2021
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	*the pedigree is complete, that is all individuals occurring as parents must have a record as individuals,		*the pedigree is complete, that is all individuals occurring as parents must have a record as individuals,
	*missing parents are coded with zero		*missing parents are coded with zero
			*the pedigree must not contain cycle dependencies

	It is not necessary that the pedigree is sorted or that a sorting variable(e.g. date of birth) is supplied.		It is not necessary that the pedigree is sorted or that a sorting variable(e.g. date of birth) is supplied.

Boerner at 05:59, 3 January 2021

2021-01-03T05:59:33Z

← Older revision		Revision as of 05:59, 3 January 2021
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	The meta-founder concept is very similar to the genetic group concept with the phantom parents becoming meta-founders, and therefore the same format requirements as for the genetic group pedigree apply. The number of meta-founders as well as the meta-founder co-variance matrix are communicated to {{lmt}} as extra parameters at the appropriate location in the parameter file.		The meta-founder concept is very similar to the genetic group concept with the phantom parents becoming meta-founders, and therefore the same format requirements as for the genetic group pedigree apply. The number of meta-founders as well as the meta-founder co-variance matrix are communicated to {{lmt}} as extra parameters at the appropriate location in the parameter file.

	== genotype file ==		=== Genotype cross-reference file ===
			The file contains the pedigree ids of the genotyped individuals as a single column vector. The genotype file and the cross-reference file must have the same number of lines. {{lmt}} will related the individual id and the genotype via the file line number, that is the pedigree id located in line #5 of the cross-reference file is that of an individual of which genotype is located in line #5 of the genotype file.

			== Genotype file ==

	A genotype file must be in ascii text format where each line contains a single genotype coded 0,1 or 2 for homozygous "aa", heterozygous "Aa" and homozygous "AA", respectively. Currently, missing values are not supported. A single genotype must not contain any space. The file must have a many lines as there are genotypes and each genotype must have the same number of markers. A file containing 10 genotypes of 40 markers each maybe		A genotype file must be in ascii text format where each line contains a single genotype coded 0,1 or 2 for homozygous "aa", heterozygous "Aa" and homozygous "AA", respectively. Currently, missing values are not supported. A single genotype must not contain any space. The file must have a many lines as there are genotypes and each genotype must have the same number of markers. A file containing 10 genotypes of 40 markers each maybe