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fix a bug caused by a change of default value used for stringsAsFactors… #5

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fix a bug caused by a change of default value used for stringsAsFactors… #5

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36 changes: 18 additions & 18 deletions src/prepare-meta-abide.R
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Original file line number Diff line number Diff line change
Expand Up @@ -10,11 +10,11 @@ get.script.dir <- function(){
script.name <- sub(file.arg.name, "", initial.options[grep(file.arg.name, initial.options)])
sourceDir <- getSrcDirectory(function(dummy) {dummy})
if (length(script.name)) { # called from command
(dirname(script.name))
(dirname(script.name))
} else if (nchar(sourceDir)) { # called with source
sourceDir
sourceDir
} else if (rstudioapi::isAvailable()) { # called from RStudio
dirname(rstudioapi::getSourceEditorContext()$path)
dirname(rstudioapi::getSourceEditorContext()$path)
} else getwd()
}

Expand Down Expand Up @@ -51,11 +51,13 @@ meta.dir <- file.path(base.dir, "data", "meta-analysis")


# table import
data.jmp <- read.xport(file.path(abide.dir, "cerebellum.stx"))
data.jmp <- read.xport(file.path(abide.dir, "cerebellum.stx"), stringsAsFactors=T)

# quality check filter
df <- subset(data.jmp, CBANALYS == "Include")
# split data frame by site
ds <- split(df, df$SITE_ID2)
# split each sub data frame by diagnosis group
dg <- lapply(ds, function(x) split(x, x$DX_GROUP))

# no quality check filter
Expand All @@ -76,24 +78,24 @@ write.table(data, file.path(abide.dir, "data-abide.txt"), row.names=F, quote=F,

# Stouffer method for combining p-values
stouffer=function(p.values, weights) {
pnorm(sum(weights*qnorm(p.values),na.rm=TRUE)/sqrt(sum(weights[!is.na(p.values)]^2)))
pnorm(sum(weights*qnorm(p.values),na.rm=TRUE)/sqrt(sum(weights[!is.na(p.values)]^2)))
}

score <- function(s2) {
# Fisher's exact test
ni <- sapply(s2, sapply, nrow)
# Fisher's exact test
ni <- do.call(cbind, lapply(s2, sapply, nrow))
psr <- fisher.test(ni)$p.value

# Student test
pmd <- sapply(c(m=1, f=2), function(i)
if (rowSums(ni)[i]==0) 1 else
t.test(s2$ASD[[i]]$AGE_AT_S, s2$Control[[i]]$AGE_AT_S)$p.value)
if (rowSums(ni)[i]==0) 1 else
t.test(s2$ASD[[i]]$AGE_AT_S, s2$Control[[i]]$AGE_AT_S)$p.value)
pmdc <- stouffer(pmd, rowSums(ni))

# F-test of equality of variances
pvr <- sapply(c(m=1, f=2), function(i)
if (rowSums(ni)[i]==0) 1 else
var.test(s2$ASD[[i]]$AGE_AT_S, s2$Control[[i]]$AGE_AT_S)$p.value)
if (rowSums(ni)[i]==0) 1 else
var.test(s2$ASD[[i]]$AGE_AT_S, s2$Control[[i]]$AGE_AT_S)$p.value)
pvrc <- stouffer(pvr, rowSums(ni))

min(psr, pmdc, pvrc)
Expand All @@ -102,16 +104,16 @@ score <- function(s2) {
dg2 <- lapply(dg, function(s) {
s2 <- lapply(s, function(x) split(x, x$SEX))
while (T) {
# Contingency table in function of diagnosis and sex
ni <- sapply(s2, sapply, nrow)
# effecive of smaller group by sex
# Contingency table in function of diagnosis and sex
ni <- do.call(cbind, lapply(s2, sapply, nrow))
# effective of smaller group by sex
ns <- apply(ni, 1, min)
# if one group by sex is too small, restore individuals for the other sex and remove individuals for that sex
sup <- ns < 3 & ns > 0
if (sum(sup) == 1)
s2 <- lapply(s, function(x) split(x, x$SEX))
s2 <- lapply(s, function(x) split(x, x$SEX))
s2 <- lapply(s2, function(x) {x[sup] <- lapply(x[sup], function(y) y[0,]); x})
ni <- sapply(s2, sapply, nrow)
ni <- do.call(cbind, lapply(s2, sapply, nrow))

s <- lapply(s2, do.call, what=rbind)
if (nrow(s$ASD) < 2 | nrow(s$Control) < 2)
Expand Down Expand Up @@ -149,5 +151,3 @@ write.table(data.Cbl_WM, file.path(meta.dir, "means-abide-Cbl_WM.txt"), row.name

data.Cbl_GM <- na.omit(datatable(dg2, "CBGM"))
write.table(data.Cbl_GM, file.path(meta.dir, "means-abide-Cbl_GM.txt"), row.names=F, quote=F, sep="\t")