cross2int(wgaim)
cross2int()所属R语言包：wgaim
Convert a cross genetic object to an interval object
转换交叉遗传的间隔对象的对象
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Converts an object of class "cross" to an object with class "interval". The function also imputes missing markers.
转换类的一个对象“cross”类的对象“interval”。功能也归咎于缺少的标记。
用法----------Usage----------
cross2int(fullgeno, missgeno = "MartinezCurnow", rem.mark = TRUE,
id = "id", subset = NULL)
参数----------Arguments----------
参数：fullgeno
an object of class "cross" with restrictions (see Details)
类的一个对象“cross”的限制（见详情）
参数：missgeno
a character string determining how missing values in the linkage map should be imputed. If "Broman", then missing values are imputed according to Bromans rules. If "MartinezCurnow" then missing values are imputed according to the rules of Martinez & Curnow (1994) (see reference list). The default is "MartinezCurnow" (see Details).
缺失的值确定如何在连锁图谱应归咎于一个字符串。如果“Broman”，然后遗漏值会被归咎于根据Bromans规则。如果“MartinezCurnow”遗漏值会被归咎于根据马丁内斯Curnow（1994）（见参考文献列表）的规则。默认值是“MartinezCurnow”（见详情）。
参数：rem.mark
logical value. If TRUE redundant markers are deleted and placed in the component of the object (see Details). Defaults to TRUE.
逻辑值。如果TRUE冗余标记被删除，并放置在该对象的组件（参见详细情况）。默认为TRUE的。
参数：id
a character string or name of the unique identifier for each row of genotype data (see Details). Defaults to "id"
一个字符串或名称的基因型数据，每一行的唯一标识符（见详情）。默认为“id”
参数：subset
a possible character vector naming the subset of chromosomes to be returned. Defaults to NULL implying return all chromosomes.
可能的字符向量命名的染色体要返回的子集。默认为NULL的这意味着返回所有的染色体。
Details
详细信息----------Details----------
This function provides the conversion of genetic data objects that have already been created using read.cross from Bromans qtl package to "interval" objects ready for use with wgaim.
此功能提供了转换已创建的的基因数据对象，使用read.cross，从Bromans qtl包“interval”对象准备使用wgaim的。
User should be aware that this function is restricted to populations with only two genotypes. fullgeno is checked for the the class structure c("bc","cross"). If this is not present an error is returned.
用户应该知道，这个函数被限制在人口只有两种基因型。 fullgeno检查类的结构c("bc","cross")。如果这是不存在，则返回一个错误。
During the conversion process, missing values are imputed according to the argument given by missgeno. This imputation results in a complete version of the marker data for each chromosome which is then used to create the interval data "intval". The complete marker data for each chromosome can be obtained from the "imputed.data" element of the returned list. It is therefore also possible to perform whole genome marker analysis using wgaim. See wgaim.asreml for more details.
在转换过程中，遗漏值是根据给定的参数missgeno归咎于。在一个完整的版本为每个染色体的标记数据，然后将用于创建的时间间隔数据“intval”此插补结果。可以从“imputed.data”元素返回的列表中的每个染色体的完整标记数据。因此，也可以进行全基因组标记分析使用wgaim。见wgaim.asreml更多详情。
If rem.mark = TRUE then markers that are identical are removed before missing values are imputed. The marker similarity is found by estimating recombination fractions using est.rf from the qtl package. The removed list is returned with the object and placed under "cor.markers" for inspection if required.
如果rem.mark = TRUE然后相同的标记被删除之前遗漏值的估算。通过估计重组率使用的标记相似est.rfqtl包。被删除的列表，则返回的对象，并放置在“cor.markers”检查，如果需要的话。
值----------Value----------
a list of class "cross" that also inherits the class "interval". The list contains the following components
一类“列表cross”也继承了类“interval”。该列表包含以下组件
参数：geno
This is a list with elements named by the corresponding names of the chromosomes. Each chromosome is itself a list with six elements: "data" is the actual estimated map matrix with rows as individuals named by "id" and markers as columns; "map" is a vector of marker positions on the corresponding chromosome; "imputed.data" is identical to "data" matrix but with all NA's replaced by imputed values according to the rules of "missgeno"; "dist" contains the genetic distance between adjacent markers or the genetic distances of the intervals; "theta" contains the recombination fractions for each interval; "intval" contains the recalculated intervals based on the recombination fractions and the missing marker information.
这是由染色体的相应名称命名的元素的列表。每个染色体本身就是六个元素的列表：“data”是个人命名为“id”和标记为列矩阵的行估计实际图“<X “是一个向量，相应的染色体上的标记位置”map“”imputed.data“矩阵是相同的，但与所有适用的替代估算值的规则“data”“missgeno”包含的遗传距离相邻标记间的遗传距离的间隔“”dist“包含的每一个区间的重组率“”theta“包含的重组率和丢失的标记信息的基础上重新计算的时间间隔。
参数：cor.markers
If rem.mark = TRUE, a three column matrix with each row describing which pairwise markers are correlated and what chromosome they are from.
如果rem.mark = TRUE，三列的矩阵每行描述成对标记是相关的，他们是从什么染色体。
参数：pheno
A data.frame of phenotypic information with rows as individuals read in from read.cross. A copy of the column named by the "id" argument can be found here (see read.cross).
数据框的表型信息与个人阅读read.cross行。副本的列名为“id”参数可以在这里找到（见read.cross）。
（作者）----------Author(s)----------
Julian Taylor, Simon Diffey, Ari Verblya and Brian Cullis
参考文献----------References----------
quantitative trait loci using regression mapping. Heredity, 73, 198-206.
Bi-Parental Populations Using Linear Mixed Models. Journal of Statistical Software, 40(7), 1-18. URL http://www.jstatsoft.org/v40/i07/.
by simultaneous use of the full linkage map. Theoretical And Applied Genetics, 116, 95-111.
参见----------See Also----------
read.cross
read.cross
实例----------Examples----------
## Not run: [＃不运行：]
# read in linkage map from a rotated .CSV file with "id" as the[CSV文件“ID”为阅读从一个旋转的遗传连锁图谱。]
# identifier for each unique row[为每一个独特的行标识符]
wgpath <- system.file("extdata", package = "wgaim")
racca <- read.cross("csvr", file="raccas.csv", genotypes=c("AA","AB"),
na.strings = c("-", "NA"), dir = wgpath)
raccas <- cross2int(racca, missgeno="MartinezCurnow", id = "id")
# plot linkage map[图连锁图谱]
link.map(raccas, cex = 0.5)
## End(Not run)[＃（不执行）]
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
注1：为了方便大家学习，本文档为生物统计家园网机器人LoveR翻译而成，仅供个人R语言学习参考使用，生物统计家园保留版权。
注2：由于是机器人自动翻译，难免有不准确之处，使用时仔细对照中、英文内容进行反复理解，可以帮助R语言的学习。
注3：如遇到不准确之处，请在本贴的后面进行回帖，我们会逐渐进行修订。
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发表于 2012-10-1 21:03:57
