batchTest(GWASTools)
batchTest()所属R语言包：GWASTools
Batch Effects of Genotyping
一批基因分型的影响
译者：生物统计家园网 机器人LoveR
描述----------Description----------
batchChisqTest calculates Chi-square values for batches from 2-by-2 tables of SNPs, comparing each batch with the other batches. batchFisherTest calculates Fisher's exact test values.
batchChisqTest计算批次的SNPs 2-2表的卡方值，与其他批次每个批次。 batchFisherTest计算Fisher精确的测试值。
用法----------Usage----------
batchChisqTest(genoData, batchVar,
chrom.include = 1:22, sex.include = c("M", "F"),
scan.exclude = NULL, return.by.snp = FALSE,
correct = TRUE, verbose = TRUE,
outfile = NULL)
batchFisherTest(genoData, batchVar,
chrom.include = 1:22, sex.include = c("M", "F"),
scan.exclude = NULL, return.by.snp = TRUE,
conf.int = FALSE, verbose = TRUE,
outfile = NULL)
参数----------Arguments----------
参数：genoData
GenotypeData object
GenotypeData对象
参数：batchVar
A character string indicating which annotation variable should be used as the batch.
一个字符串，指示注释变量应使用批次。
参数：chrom.include
Integer vector with codes for chromosomes to include. Default is 1:22 (autosomes). Use 23, 24, 25, 26, 27 for X, XY, Y, M, Unmapped respectively
编码为染色体，包括整数向量。默认是1:22（染色体）。使用的X，XY，Y，M 23，24，25，26，27分别为未映射
参数：sex.include
Character vector with sex to include. Default is c("M", "F"). If sex chromosomes are present in chrom.include, only one sex is allowed.
包括与性别的特征向量。默认是c（“M”的“F”）。如果性染色体是在chrom.include目前，只有一种性别是允许的。
参数：scan.exclude
An integer vector containing the IDs of scans to be excluded.
整数向量，包含扫描的ID被排除在外。
参数：return.by.snp
Logical value to indicate whether snp-by-batch matrices should be returned.
逻辑值指示是否应退还批次SNP矩阵。
参数：conf.int
Logical value to indicate if a confidence interval should be computed.
逻辑值应计算表明，如果一个置信区间。
参数：correct
Logical value to specify whether to apply the Yates continuity correction.
逻辑值，指定是否要申请耶茨连续性校正。
参数：verbose
Logical value specifying whether to show progress information.
逻辑值，指定是否显示进度信息。
参数：outfile
A character string to append in front of ".RData" for naming the output file.
在前面“。RDATA”命名输出文件追加一个字符串。
Details
详情----------Details----------
Because of potential batch effects due to sample processing and genotype calling, batches are an important experimental design factor.
由于潜在的一批影响由于来样加工和基因型分型，批次是一个重要的实验设计因子。
batchChisqTest calculates the Chi square values from 2-by-2 table for each SNP, comparing each batch with the other batches.
batchChisqTest计算每个SNP-2表2卡方值，与其他批次每批。
batchFisherTest calculates Fisher's Exact Test from 2-by-2 table for each SNP, comparing each batch with the other batches.
batchFisherTest费舍尔的计算从2-2表，每个SNP的精确测试，与其他批次每个批次。
For each SNP and each batch, batch effect is evaluated by a 2-by-2 table: # of A alleles, and # of B alleles in the batch, versus # of A alleles, and # of B alleles in the other batches. Monomorphic SNPs are set to NA for all batches.
对于每个SNP和每个批次，批次的效果进行评估，由2-2表：＃A等位基因，＃B等位基因批次中，与＃A等位基因，＃B等位基因在其他批次。单形单核苷酸多态性的所有批次设置为NA。
The default behavior is to combine allele frequencies from males and females and return results for autosomes only. If results for sex chromosomes (X or Y) are desired, use chrom.include with values 23 and/or 25 and sex.include="M" or "F".
默认行为是结合男性和女性的等位基因频率和染色体只有返回的结果。如果需要为性染色体（X或Y）的结果，使用chrom.include23和/或25sex.include=的“M”或“F”的值。
If there are only two batches, each output matrix will have only one column.
如果只有两个批次，每个输出矩阵只有一列。
值----------Value----------
If outfile=NULL (default), all results are returned as a list. If outfile is specified, no data is returned but the list is saved to disk as "outfile.RData."
如果outfile=NULL（默认），所有的结果作为一个列表返回。如果outfile指定，没有数据返回，但列表保存到磁盘“outfile.RData。”
batchChisqTest returns a list with the following elements:
batchChisqTest返回一个包含下列元素的列表：
参数：mean.chisq
a vector of mean chi-squared values for each batch.
一个向量是指每批卡方值。
参数：lambda
a vector of genomic inflation factor computed as median(chisq) / 0.456 for each batch.
median(chisq) / 0.456每批向量的基因通货膨胀因素计算。
参数：chisq
a matrix of chi-squared values with SNPs as rows and batches as columns. Only returned if return.by.snp=TRUE.
单核苷酸多态性与卡方值矩阵的行和列的批次。如果return.by.snp=TRUE只返回。
batchFisherTest returns a list with the following elements:
batchFisherTest返回一个包含下列元素的列表：
参数：mean.or
a vector of mean odds-ratio values for each batch.
一个向量是指每批胜算比值。
参数：lambda
a vector of genomic inflation factor computed as median(-2*log(pval) / 1.39 for each batch.
median(-2*log(pval) / 1.39每批向量的基因通货膨胀因素计算。
Each of the following is a matrix with SNPs as rows and batches as columns, and is only returned if return.by.snp=TRUE:
以下是一个单核苷酸多态性作为矩阵的行和列批次，仅返回如果return.by.snp=TRUE：
参数：pval
P value
P值
参数：oddsratio
Odds ratio
胜算比
参数：confint.low
Low value of the confidence interval for the odds ratio. Only returned if conf.int=TRUE.
低附加值的胜算比的置信区间。如果conf.int=TRUE只返回。
参数：confint.high
High value of the confidence interval for the odds ratio. Only returned if conf.int=TRUE.
高价值的胜算比的置信区间。如果conf.int=TRUE只返回。
batchChisqTest and batchFisherTest both also return the following if return.by.snp=TRUE:
batchChisqTest和batchFisherTest也都返回以下return.by.snp=TRUE：
参数：allele.counts
matrix with total number of A and B alleles over all batches.
矩阵A和B等位基因对所有批次的总数。
参数：min.exp.freq
matrix of minimum expected allele frequency with SNPs as rows and batches as columns.
矩阵的最低预期与单核苷酸多态性的等位基因频率为行和列批次。
Warnings:
警告：
If outfile is not NULL, another file will be saved with the name "outfile.warnings.RData" that contains any warnings generated by the function.
如果outfile是不是NULL，另一个文件将被保存的名称为“outfile.warnings.RData”，它包含的功能产生任何警告。
作者（S）----------Author(s)----------
Xiuwen Zheng, Stephanie Gogarten
参见----------See Also----------
GenotypeData, chisq.test, fisher.test
GenotypeData，chisq.test，fisher.test
举例----------Examples----------
library(GWASdata)
file <- system.file("extdata", "affy_geno.nc", package="GWASdata")
nc <- NcdfGenotypeReader(file)
data(affy_scan_annot)
scanAnnot <- ScanAnnotationDataFrame(affy_scan_annot)
genoData <- GenotypeData(nc, scanAnnot=scanAnnot)
# autosomes only, sexes combined (default)[染色体只，两性结合（默认）]
res.chisq <- batchChisqTest(genoData, batchVar="plate")
res.chisq$mean.chisq
res.chisq$lambda
# X chromosome for females[X染色体为女性]
res.chisq <- batchChisqTest(genoData, batchVar="status",
chrom.include=23, sex.include="F", return.by.snp=TRUE)
head(res.chisq$chisq)
# Fisher exact test of "status" on X chromosome for females[Fisher精确检验为女性的X染色体上的“状态”]
res.fisher <- batchFisherTest(genoData, batchVar="status",
chrom.include=23, sex.include="F")
qqPlot(res.fisher$pval)
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 21:22:18
