# running average standard deviation
xxx <- S.sd[!is.na(S.sd)][order(index.col[!is.na(S.sd)])]
- xxx <- _runavg(xxx, winsize)
+ xxx <- runavg(xxx, winsize)
xxx <- xxx[rank(index.col[!is.na(S.sd)])]
S.rasd <- rep(NA, nrow(h))
S.rasd[!is.na(S.sd)] <- xxx
## average expression level and the running average calculated on
## the estimated st. dev. for each locus. All the wierd code is a
## work around of missing values
- cont.sd.runavg <- _runavg(cont.sd[order(cont.mean)])[order(order(cont.mean))]
- exp.sd.runavg <- _runavg( exp.sd[order( exp.mean)])[order(order( exp.mean))]
+ cont.sd.runavg <- runavg(cont.sd[order(cont.mean)])[order(order(cont.mean))]
+ exp.sd.runavg <- runavg( exp.sd[order( exp.mean)])[order(order( exp.mean))]
## xxx <- temp5[!is.na(temp5)][order(temp3[!is.na(temp5)])]
- ## xxx <- _runavg(xxx, winsize)
+ ## xxx <- runavg(xxx, winsize)
## xxx <- xxx[rank(temp3[!is.na(temp5)])]
## temp11 <- rep(NA, nrow(h))
## temp11[!is.na(temp5)] <- xxx
## xxx <- temp6[!is.na(temp6)][order(temp4[!is.na(temp6)])]
- ## xxx <- _runavg(xxx, winsize)
+ ## xxx <- runavg(xxx, winsize)
## xxx <- xxx[rank(temp4[!is.na(temp6)])]
## temp12 <- rep(NA, nrow(h))
## temp12[!is.na(temp6)] <- xxx
- cont.sd.log.runavg <- _runavg(cont.sd.log[order(cont.mean.log)])[order(order(cont.mean.log))]
- exp.sd.log.runavg <- _runavg( exp.sd.log[order( exp.mean.log)])[order(order( exp.mean.log))]
+ cont.sd.log.runavg <- runavg(cont.sd.log[order(cont.mean.log)])[order(order(cont.mean.log))]
+ exp.sd.log.runavg <- runavg( exp.sd.log[order( exp.mean.log)])[order(order( exp.mean.log))]
## xxx <- temp9[!is.na(temp9)][order(temp7[!is.na(temp9)])]
- ## xxx <- _runavg(xxx, winsize)
+ ## xxx <- runavg(xxx, winsize)
## xxx <- xxx[rank(temp7[!is.na(temp9)])]
## ## like 11 and 12 but for the log transofrmed data
## temp13 <- rep(NA, nrow(h))
## temp13[!is.na(temp9)] <- xxx
## xxx <- temp10[!is.na(temp10)][order(temp8[!is.na(temp10)])]
- ## xxx <- _runavg(xxx, winsize)
+ ## xxx <- runavg(xxx, winsize)
## xxx <- xxx[rank(temp8[!is.na(temp10)])]
## temp14 <- rep(NA, nrow(h))
## temp14[!is.na(temp10)] <- xxx
}
-_runavg <- function(x,k=1){
+runavg <- function(x,k=1){
if (k < 0)
stop("k must be greater than or equal to 0");
if (k==0)