compSetStats: Compute sample statistics

In tonedivad/GRMeta: Processing MetX data

Description

Compute sample statistics in a metaboSet object

Usage

compSetStats(obj, lStats = list(),sType=NULL,Sids=NULL,addtoname=NULL,addtoobject=FALSE)

Arguments

obj	metaboSet object
lStats	List of stats to be performed
sType	sType level for samples
Sids	List Sids for the calculation
addtoname	Concatenate string to the begining of the stat names
addtoobject	If TRUE the stats will be added to the obj$Annot and the result object returned

Value

Matrix of stats or metaboSet object

Author(s)

David Enot [e-mail]

Examples

(testfiles=list.files(system.file( package = "GRMeta"),pattern = "txt$",full.names = TRUE))
mydata=loadAgilentData(ifile =testfiles[1])
mydata

##### Use sample of sType=="St"
##### Number with Height>0,  Height>100 | Proportion with Height>0,  Height>100  | Proportion of non-NA with Height>0,  Height>100 
lStats=list(c("Sum","Height>0"),c("Sum","Height>100"),c("Prop","Height>0"),c("Prop","Height>100"),
c("PropNNA","Height>0"),c("PropNNA","Height>100"))
result=compSetStats(mydata,lStats=lStats,sType="St")
head(result)

##### Same results if actual Sid are given
lSamp=mydata$Sid[mydata$Meta$sType=="St"]
result=compSetStats(mydata,lStats=lStats,Sids=lSamp)
head(result)


##### Compute CVs on QCwith at least 1 non NAs or at least 5 and add "myQC" before the column name
result=compSetStats(mydata,lStats=list(c("CV","Area",1),c("CV","Area",5)),sType="QC",addtoname="myQC")
head(result)

##### Compute CVs on QC with at least 2 non NAs and check the number of "St" with SBR>5 / add to the object
mydata2=compSetSBR(mydata,thresh=10,SidBlank = c("Bl_prerun-eau_1","Bl_prerun-eau_1b"),newname = "SBR")
## Compute CVs on QC with at least 2 non NAs
mydata3=compSetStats(mydata2,lStats=list(c("CV","Area",2)),sType="QC",addtoname="myQC",addtoobject=TRUE)
## Compute on St: CV with at least 2 non NAs, number of SBR>5 and number of non missing
mydata3=compSetStats(mydata3,lStats=list(c("CV","Area",2),c("Sum","SBR>5"),c("Sum","Height>0")),sType="St",addtoname="myST",addtoobject=TRUE)
head(mydata3$Annot)

l2rm=mydata3$Analyte[which(mydata3$Annot$myQC_CV_Area_2>20 | mydata3$Annot$`myST_Sum_SBR>5`==0)]
deleteEntries(mydata3,Analyte=l2rm)

#############################################
## Looping over each sType for e.g.
mydata4=mydata2
for(i in unique(mydata4$Meta$sType))
    mydata4=compSetStats(mydata4,lStats=list(c("CV","Area",0),
    c("Sum","SBR>5"),c("Sum","Height>0")),
    Sids=mydata4$Sid[mydata4$Meta$sType==i],addtoname=i,addtoobject=TRUE)

## before:
head(mydata2$Annot)

## after:
head(mydata4$Annot)

tonedivad/GRMeta documentation built on May 31, 2019, 6:21 p.m.