annotateDiffreport(CAMERA)
annotateDiffreport()所属R语言包：CAMERA
Automatic deconvolution/annotation of LC/ESI-MS data
的LC / ESI-MS的数据自动卷积/注释
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Wrapper function for the xcms diffreport and the annotate function. Returns a diffreport within the annotation results.
包装功能为xcms diffreport和批注功能。返回内的注解结果一个diffreport。
用法----------Usage----------
annotateDiffreport(object, sample=NA, nSlaves=1, sigma=6, perfwhm=0.6,
cor_eic_th=0.75, graphMethod="hcs", pval=0.05, calcCiS=TRUE,
calcIso=FALSE, calcCaS=FALSE, maxcharge=3, maxiso=4, minfrac=0.5,
ppm=5, mzabs=0.015, quick=FALSE, psg_list=NULL, rules=NULL,
polarity="positive", multiplier=3, max_peaks=100, intval="into",
pval_th = NULL, fc_th = NULL, sortpval=TRUE, ...)
参数----------Arguments----------
参数：object
xcmsSet with peak group assignments
与峰集团转让xcmsSet
参数：sample
xsAnnotate: Sample selection for grouped xcmsSet, see xsAnnotate-class
xsAnnotate：样本分组xcmsSet的选择，看到xsAnnotate级
参数：nSlaves
xsAnnotate: Use parallel CAMERA mode, require Rmpi
xsAnnotate：使用并行相机的模式，需要Rmpi
参数：sigma
groupFWHM: multiplier of the standard deviation
groupFWHM：乘数的标准偏差
参数：perfwhm
groupFWHM: percentage of FWHM width
groupFWHM：半高宽宽度的百分比
参数：cor_eic_th
groupCorr: correlation threshold (0..1)
groupCorr：相关阈值（0 .. 1）
参数：graphMethod
groupCorr: Method selection for grouping peaks after correlation analysis into pseudospectra
groupCorr：分组相关分析后，将伪谱峰方法的选择
参数：pval
groupCorr: significant correlation threshold
groupCorr：显着相关性阈值
参数：calcCiS
groupCorr: Use correlation inside samples for peak grouping
groupCorr：样本内使用高峰分组相关
参数：calcIso
groupCorr: Use isotopic relationship for peak grouping
groupCorr：使用同位素峰分组的关系
参数：calcCaS
groupCorr: Use correlation across samples for peak grouping
groupCorr：跨样本的使用高峰分组相关
参数：maxcharge
findIsotopes: max. ion charge
findIsotopes：最大。离子电荷
参数：maxiso
findIsotopes: max. number of expected isotopes
findIsotopes：最大。预期同位素数
参数：minfrac
findIsotopes: The percentage number of samples, which must satisfy the C12/C13 rule for isotope annotation
findIsotopes：样本的百分比数字，它必须满足同位素注释C12/C13规则
参数：ppm
General ppm error
一般ppm误差
参数：mzabs
General absolut error in m/z
一般绝对错误的m / z
参数：quick
Use only groupFWHM and findIsotopes
只使用groupFWHM和findIsotopes
参数：psg_list
Calculation will only be done for the selected groups
将只为选定的组进行计算
参数：rules
findAdducts: User defined ruleset
findAdducts：用户定义的规则集
参数：polarity
findAdducts: Which polarity mode was used for measuring of the ms sample
findAdducts：ms采样测量极性模式
参数：multiplier
findAdducts: If no ruleset is provided, calculate ruleset with max. number n of [nM+x] clusterions
findAdducts：如果没有提供规则集，计算出最大的规则集。数N [NM + X] clusterions
参数：max_peaks
How much peaks will be calculated in every thread using the parallel mode
多少峰将在每一个使用线程并行模式计算
参数：intval
General used intensity value (into, maxo, intb)
一般使用的强度值（进，maxo，INTB）
参数：pval_th
pval threshold. Creates a new psg_list. A pseudospectra is selected if it contains peaks, with pval < pval_th
pval的阈值。创建一个新psg_list。一个伪谱被选中，如果它包含的山峰，pval的<pval_th
参数：fc_th
Same as pval. Select those groups with contains peaks with fold-change > fc_th. Pval_th and fc_th can be combined
作为pval的相同。选择这些群体包含倍变化> fc_th峰。可以结合pval_th和fc_th
参数：sortpval
Sort diffreport after pvalues
排序diffreport后pvalues
参数：...
Diffreport parameters see diffreport
diffreport参数见diffreport
Details
详情----------Details----------
Batch script wrapper for combining the annotation and the diffreport for a (grouped) xcmsSet xs. Function list: 1: diffreport(), 2: groupFWHM(), 3: findIsotopes(), 4: groupCorr(), 5: findAdducts() For a speedup calculation users can create a quick run, with quick = TRUE to preselect pseudospectra of interest. The indices of those pseudospectra are set with psg_list in a second run. On the other hand, a automatic selection with pval_th and/or fc_th can be performed. Returns the normal xcms diffreport table, with the additional CAMERA slots
结合注释和（分组）xcmsSetxsdiffreport批处理脚本包装。功能列表：1：diffreport（），2：groupFWHM（），3：findIsotopes（），4：groupCorr（），5：findAdducts（对于加速计算用户）可以创建一个快速运行，快速= TRUE预选伪谱利益。这些伪谱指数在第二次运行psg_list。另一方面，可以进行自动选择与pval_th和/或fc_th的。返回正常xcms diffreport的表，额外的相机插槽
值----------Value----------
annotateDiffreport returns an diffreport, see diffreport, within additional columns containing the annotation results.
annotateDiffreport返回一个diffreport，看到diffreport内额外的列包含注释的结果。
作者（S）----------Author(s)----------
Carsten Kuhl <ckuhl@ipb-halle.de>
举例----------Examples----------
#Multiple sample [多个样品]
library(CAMERA)
library(faahKO)
xs.grp <- group(faahko)
xs.fill <- fillPeaks(xs.grp)
#fast preselection[快速预选]
# diffreport <- annotateDiffreport(xs.fill,quick=TRUE)[< - annotateDiffreport diffreport（xs.fill，快速= TRUE）]
# index <- c(1,18,35,45,56) #Make only for those grps a adduct annotation[指数< - C（1,18,35,45,56）＃只对那些GRPS 1加合物的注解]
# diffreport2 <- annotateDiffreport(xs.fill,psg_list=index,metlin = TRUE)[diffreport2 < - annotateDiffreport（xs.fill，psg_list =指数，METLIN = TRUE）]
#automatic selection for groups with peaks p-val < 0.05 and fold-change > 3[自动选择与峰组的P-值<0.05倍变化> 3]
# diffreport <- annotateDiffreport(xs.fill,pval_th=0.05,fc=3)[< - annotateDiffreport diffreport（xs.fill，pval_th = 0.05，FC = 3）]
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 2012-2-25 14:02:36
