# R/metaSubF.R In MetaCycle: Evaluate Periodicity in Large Scale Data

```### Authors of original code of fisher's method: Karl Kugler <[email protected]>, and Laurin AJ Mueller and Armin Graber
### Citation: MADAM - An Open Source Toolbox for Meta-Analysis. Source Code for Biology and Medicine 2010, 5:3
### The minor modification here is removing the code associated with 'multicore' package
###======================================================================================================================================
## function to calculate fisher sum
## p: vector of p-values
fisher.sum <- function(p, zero.sub=0.00001, na.rm=FALSE){
if(any(p>1, na.rm=TRUE)||any(p<0, na.rm=TRUE))
stopifnot(zero.sub>=0 & zero.sub<=1 || length(zero.sub)!=1)
p[p==0] <- zero.sub
if(na.rm)
p<- p[!is.na(p)]
S= -2*sum(log(p))
res <- data.frame(S=S, num.p=length(p))
return(res)
}
## main function of combining p-values by performing Fisher's method
fisher.method <- function(pvals, method=c("fisher"), p.corr=c("bonferroni","BH","none"), zero.sub=0.00001, na.rm=FALSE){
stopifnot(method %in% c("fisher"))
stopifnot(p.corr %in% c("none","bonferroni","BH"))
stopifnot(all(pvals>=0, na.rm=TRUE) & all(pvals<=1, na.rm=TRUE))
stopifnot(zero.sub>=0 & zero.sub<=1 || length(zero.sub)!=1)
if(is.null(dim(pvals)))
stop("pvals must have a dim attribute")
p.corr <- ifelse(length(p.corr)!=1, "BH", p.corr)
##substitute p-values of 0
pvals[pvals == 0] <- zero.sub
fisher.sums <- data.frame(do.call(rbind, apply(pvals, 1, fisher.sum, zero.sub=zero.sub, na.rm=na.rm)))

rownames(fisher.sums) <- rownames(pvals)
fisher.sums\$p.value <- 1-pchisq(fisher.sums\$S, df=2*fisher.sums\$num.p)
none = fisher.sums\$p.value)
return(fisher.sums)
}
###======================================================================================================================================
###other functions shared by 'meta2d' and 'meta3d'
##adjusting phase with period length, eg. transfer phase from '26h' to '2h', if period length is 24h.
{
###adjusting phase with expected period length
subper <- as.numeric(subper);
} else if ( ( is.numeric(adjustV) ) & (adjustV > 0) ) {
} else {
return(as.numeric(subpha));
}
subpha <- as.numeric(subpha);
pha_fold <- floor(subpha/subper);
}
##calculate the mean phase of multiple phases from different methods using 'mean of circular quantities'
circularMean <- function (z, subper, zweit, meanper, subadj)
{
if ( length(z) > 0 )  {
if (sum(zweit) > 0)
{
{
{
##subadj = 0 (indicating no adjustment of phase), return linear mean values
zmean <- sum(z*zweit)/sum(zweit);
return(zmean);
} else {
stop( c("There is unknown bug associated with 'circularMean()'. ",
}
}

##convert phase values to polar coordinates
##for 'predictedPer', 'subper' here is period length from each method
zpolar <- z/subper*2*pi;
##another strategy may use the same 'meanper' value for different methods (subper=meanper), which seems less reasonable
##eg. if 'meanper'=25, the max per for JTK is 24 (one cycle sampling), it seems more reasonable to
##use predicted period by JTK for transferring its phase values to polar values than using the 'meanper'.

##convert polar coordinates to cartesian coordinates
siny <- sum(sin(zpolar)*zweit);
cosx <- sum(cos(zpolar)*zweit);
##siny and cosx are not divided by 'sum(zweit)'; 'y/x' will get the same result if divided or not divided by the same value

##get mean of circular quantities
meanpolar <- atan2(siny, cosx);

##convert to the mean phase value
meanpha <- meanpolar/(2*pi)*meanper;
if (meanpha < 0)
{ meanpha <- meanpha +  meanper;  }
return(meanpha);
}  else  {
return(NaN);
}
}  else {
return(NaN);
}
}
##extract the field separator character(FILE_SEP), the set of quoting
##characters(FILE_QUOTE), the character used for decimal points(FILE_DEC).
getFileSignF <- function(filestyle)
{
file_quote2 <- FALSE;
if (length(filestyle) == 1) {
if (filestyle=="csv") {
file_sep <- ",";
file_quote <- "\"";
file_quote2 <- TRUE;
file_dec <- ".";
} else if (filestyle=="txt") {
file_sep <- "\t";
file_quote <- "";
file_dec <- ".";
} else {
stop(c("Please set 'filestyle' before running this function ",
"(the 'filesyle' could be set as 'txt' or 'csv').\n") );
}
} else if (length(filestyle) > 1) {
if (length(filestyle) == 3) {
file_sep <- filestyle[1];
file_quote <- filestyle[2];
file_quote2 <- TRUE;
file_dec <- filestyle[3];
} else {
stop(c("Please set 'filestyle' before running this function ",
"(the 'filesyle' should be assigned a vector containing ",
"three characters, which corresponding to symbols used to ",
"separate columns, quote values and used for decimal points).\n") );
}
} else {
stop(c("Please set 'filestyle' before running this function ",
"(the 'filesyle' could be set as 'txt' or 'csv', or could be ",
"assigned a vector containing three characters, ",
"which corresponding to symbols used to separate columns, ",
"quote values and used for decimal points).\n") );
}
return(list("sep"=file_sep, "quote"=file_quote, "quote2"=file_quote2, "dec"=file_dec))
}
###======================================================================================================================================
```

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MetaCycle documentation built on May 29, 2017, 9:38 p.m.