Pedigree(GeneticsPed)
Pedigree()所属R语言包：GeneticsPed
Pedigree
系谱
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Pedigree function creates a pedigree object
Pedigree函数创建一个谱系的对象
用法----------Usage----------
Pedigree(x, subject="id", ascendant=c("father", "mother"),
ascendantSex=c(1, 2), ascendantLevel=c(1, 1), unknown=NA, sex=NA,
dtBirth=NA, generation=NA, family=NA, generationOrder="increasing",
check=TRUE, sort=FALSE, extend=FALSE, drop=TRUE, codes=FALSE)
参数----------Arguments----------
参数：x
data.frame or matrix
数据框或矩阵
参数：subject
character, column name in x for subjects
字符，x科目列名
参数：ascendant
character, column name(s) in x for ascendants
字符，列名在x（S）为长辈
参数：family
character, column name in x for family
字符，x列名家庭
参数：ascendantSex
integer orcharacter, sex of ascendant(s); see details
orcharacter整数，方兴未艾的性别（S）;查看详细信息
参数：ascendantLevel
integer, generation level of ascendant(s); see details
整数，代水平的方兴未艾（S）;见详情
参数：unknown
vector or list, uknown representation of identification and other data in the pedigree; see details
向量或列表，uknown系谱鉴定和其他数据的代表性;查看详细信息
参数：sex
character, column name in x for sex
字符，在x列名性别
参数：dtBirth
character, column name in x for date of birth
字符，x列名，出生日期
参数：generation
character, column name in x for generation
字符，x发电的列名
参数：generationOrder
character, generation value is "increasing" or "decreasing" through generations; see details
性格，代值“增加”或“下降”，通过几代人;见详情
参数：check
logical, check for common errors
逻辑，检查的常见错误
参数：sort
logical, sort pedigree
逻辑，排序系谱
参数：extend
logical, extend pedigree
逻辑，扩展系谱
参数：drop
logical, drop unused levels if factors are used
逻辑，删除未使用的水平，如果使用的因素
参数：codes
logical, code individuals into integers
逻辑，代码为整数个人
Details
详情----------Details----------
FIXME: study geneSet class
FIXME：为的研究geneSet类
Pedigree can be one source of information on genetic relationship between relatives. Take for example the following pedigree:
家谱可以是亲属之间的亲缘关系的信息来源之一。采取以下的血统为例：
There is considerable variability in terminology between as well as within various fields of genetics. We use the following terms throughout the help and code: individual (any individual in a pedigree), subject (individual whose pedigree is given i.e. individuals in the first column in upper data.frame), ascendant and descendant. Additionally, family, sex, dtBirth and generation are used for additional data in the pedigree. Their meaning should be clear. For these, argument col is usually used in function calls.
有相当大的变化之间以及在各个领域的遗传学术语。我们整个的帮助和代码中使用下列用语：个人（在谱系的任何个人），主体（人的血统，即在数据框上的第一列个人），方兴未艾的后裔。此外，用于家庭，性别，dtBirth和代血统的额外数据。应该清楚自己的意思。这些参数col通常是用在函数调用。
family TODO
family的TODO
ascendantSex can be used to define sex of ascendant(s); for example c("Male", "Female") or c("M", "F") or even c(1, 2) for father and mother or c(2, 1, 1) for mother and two possible fathers or c(1, 1) for father and maternal father etc. This data is needed only for the structure of the class and defaults should be ok for the majority. But you need to make sure that data defined here must be in accordance with values in sex column.
ascendantSex可以用来定义方兴未艾的性别（S）;例如c（“男”，“女”）或C（“M”的“F”），或即使C（1， 2）父亲和母亲或c（2，1，1）对母亲，父亲和母亲的父亲等两个可能的父亲或C（1，1）此数据只需要为结构类和默认应该确定为多数。但是，你需要确保这里定义的数据必须是按照sex列中的值。
ascendantLevel can be used to define generation level of ascendant(s) in relation to a subject; for example c(1, 1) for father and mother or c(1, 1, 1) for mother and two possible fathers or c(1, 2) for father and maternal father etc. This data is needed only for the structure of the class and defaults should be ok for the majority.
ascendantLevel可以用来定义代的水平，在关系到一个主题方兴未艾（S）;例如C的父亲和母亲或c（1，1，1）（1，1）的母亲和两个可能的父亲等数据只需要为结构类和默认的父亲和母亲的父亲或c（1，2）应确定为多数。
There is no need for as.integer TODO in arguments ascendantLevel as this is done internally.
有没有参数需要as.integer的TODO ascendantLevel，因为这是在内部完成。
unknown TODO
未知的TODO
Sex TODO
性别的TODO
Date of birth TODO
日期出生的TODO
generationOrder defines in which order are generation values: "increasing" if values increase from ascendants to descendants and "decreasing" if values decrease from ascendants to descendants.
generationOrder定义的顺序是generation值：“增加”，如果值增加从祖先后裔和“减少”，如果值降低从祖先到后代。
check, sort, extend, and codes are actions on the pedigree and have their own help pages.
check，sort，extend，codes系谱上的行动，并有自己的帮助页面。
Individuals can be stored as either integer, numeric or factor TODO. In any case all id columns must have the same class and this is automatically checked. Argument drop can be used to drop unused levels, if factors are used.
个人可以存储为任何整数，数字或因素的TODO。在任何情况下，所有的ID列必须具有相同的类，这是自动检查。参数drop可以用于删除未使用的水平，如果使用的因素。
as.Pedigree.* FIXME as.*.Pedigree FIXME
as.Pedigree.*FIXMEas.*.PedigreeFIXME
Object of Pedigree class is a data.frame with columns that can be divided into core columns (subject, ascendant(s), sex, dtBirth and generationTODO) and possibly other columns such as data on phenotype and genotype and other subject attributes, for example factors and covariates TODO. Class name starts in upper case i.e. &ldquo edigree” and not “pedigree”, due to name clash with similar function in kinship package.
谱系类的对象是一个可以划分成芯柱（主体，方兴未艾（S），性别，dtBirth和generationTODO）和其他可能的列，如表型和基因型与其他学科的属性数据的列的数据框，例如因素和协变量的TODO。类的名字开始即在大写的“开山鼻祖”，而不是“开山鼻祖”，由于具有类似的功能kinship包命名冲突。
Additionally, the following attributes are set on pedigree:
此外，下面的属性设置系谱：
.subjectcharacter, column name of subject identification in pedigree
subjectcharacter，主体识别的名字列在谱系
.ascendantcharacter, column name(s) of ascendant(s) identification in pedigree
。ascendantcharacter，列名的系谱鉴定方兴未艾（S）（S）
.familycharacter, column name of family identification in pedigree
familycharacter，家族识别的名称列在谱系
.ascendantSexinteger, sex of ascendant(s)
。ascendantSexinteger，方兴未艾的性别（）
.ascendantLevelinteger, generation level of ascendant(s)
ascendantLevelinteger，方兴未艾的代水平（）
.sexcharacter, column name of subject's sex
。sexcharacter，列名受测者的性别
.dtBirthcharacter, column name of subject's date of birth
主体的出生日期，列名称。dtBirthcharacter
.generationcharacter, column name of subject's generation
主体的一代，列名称。generationcharacter
.generationOrdercharacter, generation value is "increasing" or "decreasing" through generations
。generationOrdercharacter，代值“增加”或“下降”，通过几代人
.colClasscharacter, storage class for id columns: "integer", "numeric" or "factor"
。colClasscharacter，存储类ID列：“整数”，“数字”或“因子”
.checkedlogical, is pedigree checked for common errors
系谱。checkedlogical，检查常见错误
.sortedlogical, is pedigree sorted; by TODO
sortedlogical，谱系排序;由待办事项
.extendedlogical, is pedigree extended
extendedlogical，谱系延长
.codedlogical, is pedigree coded
codedlogical，血统编码
.unknownlist, uknown representation for individual identification and other data in the pedigree; names of the list are c(".id", ".family", ".sex", ".dtBirth", ".generation")
个体识别和其他数据的系谱。，uknown表示unknownlist;列表中的名称是c（“ID”，“家庭”，“性”，“dtBirth。”一代。“ ;)
值----------Value----------
Pedigree object as described in the details
谱系对象中所述的细节
作者（S）----------Author(s)----------
Gregor Gorjanc
参见----------See Also----------
check, sort, and extend provide help on pedigree utility functions. There is also pedigree in kinship package
check，sort，extend系谱实用功能提供帮助。还有pedigreekinship包
举例----------Examples----------
data(Mrode2.1)
Mrode2.1$dtB <- as.Date(Mrode2.1$dtB)
x2.1 <- Pedigree(x=Mrode2.1, subject="sub", ascendant=c("fat", "mot"),
ascendantSex=c("M", "F"), family="fam", sex="sex",
generation="gen", dtBirth="dtB")
if (FALSE) {
## How to handle different pedigree types[＃如何处理不同的谱系类型]
## * multiple parents[＃*多个家长]
ped2 <- ped
ped2$father1 <- ped$father
ped2$father2 <- ped$father
ped2$father <- NULL
ped2 <- as.data.frame(ped2)
str(Pedigree(ped2, ascendant=c("father1", "father2", "mother"),
ascendantSex=c(1, 1, 2), ascendantLevel=c(1, 1, 1)))
## * different level of parents[＃*不同层次的家长]
ped3 <- as.data.frame(ped)
ped3$m.grandfather <- ped3$mother
ped3$mother <- NULL
str(Pedigree(ped3, ascendant=c("father", "m.grandfather"),
ascendantSex=c(1, 1), ascendantLevel=c(1, 2)))
}
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。
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发表于 2012-2-25 19:08:06
