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Fix proportion estimation for NA values #31

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Fix proportion estimation for NA values #31

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567db9c
Fix proportion estimation for NA values
yoda-vid Jun 9, 2022
4793fc9
Fix attempting to remove NAs when none are present
yoda-vid Jul 14, 2022
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21 changes: 18 additions & 3 deletions R/Deconvolution.R
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Original file line number Diff line number Diff line change
Expand Up @@ -597,12 +597,19 @@ SCDC_prop <- function (bulk.eset, sc.eset, ct.varname, sample, ct.sub, iter.max
prop.est.mvw <- NULL
yhat <- NULL
yhatgene.temp <- rownames(basis.mvw)
to.remove <- list()
for (i in 1:N.bulk) {
basis.mvw.temp <- basis.mvw
xbulk.temp <- xbulk[, i]*100
sigma.temp <- sigma
com.genes <- sum(xbulk[, i] != 0)
message(paste(colnames(xbulk)[i], "has common genes",
sum(xbulk[, i] != 0), "..."))
com.genes, "..."))
if (is.na(com.genes)) {
# store indices of NA vals to remove later
to.remove <- append(to.remove, -i)
next
}
lm <- nnls::nnls(A = basis.mvw.temp, b = xbulk.temp)
delta <- lm$residuals
wt.gene <- 1/(nu + delta^2 + colSums((lm$x * ALS.S)^2 *
Expand Down Expand Up @@ -640,9 +647,17 @@ SCDC_prop <- function (bulk.eset, sc.eset, ct.varname, sample, ct.sub, iter.max
])
}
colnames(prop.est.mvw) <- colnames(basis.mvw)
rownames(prop.est.mvw) <- colnames(xbulk)
colnames(yhat) <- colnames(xbulk)

# remove column names for NA vals
xbulk.cols <- colnames(xbulk)
yobs <- exprs(bulk.eset)
to.remove <- unlist(to.remove)
if (!is.null(to.remove)) {
xbulk.cols <- xbulk.cols[to.remove]
yobs <- yobs[, to.remove]
}
rownames(prop.est.mvw) <- xbulk.cols
colnames(yhat) <- xbulk.cols
yeval <- SCDC_yeval(y = yobs, yest = yhat, yest.names = c("SCDC"))
peval <- NULL
if (!is.null(truep)) {
Expand Down