R/NBth.R
In Nanostring-Biostats/GeoDiff: Count model based differential expression and normalization on GeoMx RNA data
#' Negative Binomial threshold model
#'
#' Estimate the signal size factor for features above the background
#'
#' @param object a valid GeoMx S4 object
#' @param split indicator variable on whether it is for multiple slides (Yes, TRUE; No, FALSE)
#' @param features_high subset of features which are well above the background
#' @param sizefact_BG size factors for the background
#' @param sizefact_start initial value for size factors
#' @param size_scale method to scale the sizefact, sum(sizefact)=1 when size_scale="sum", sizefact[1]=1 when size_scale="first"
#' @param threshold_start initial value for threshold
#' @param threshold_fix whether to fix the threshold, default=FALSE
#' @param tol tolerance to determine convergence, default=1e-3
#' @param iterations maximum iterations to be run, default=5
#' @param start_para starting values for parameter estimation, default=c(threshold_start, 1)
#' @param lower_sizefact lower limit for sizefact, default=0
#' @param lower_threshold lower limit for threshold
#' @param ... additional argument list that might be used
#'
#' @importFrom Biobase pData
#' @importFrom Biobase fData
#' @importFrom Biobase exprs
#' @importFrom Biobase experimentData
#' @importFrom Biobase featureNames
#' @importFrom Biobase annotation
#'
#'
#' @return a valid GeoMx S4 object
#' \itemize{
#' \item para0 = "NA", in experimentData
#' \item para, estimated parameters, "signal" "r" in rows and features in columns, in featureData
#' \item sizefact, estimated size factor, in phenoData
#' \item preci1 = "NA", in experimentData
#' \item conv0 = "NA", in experimentData
#' \item conv = "NA", in experimentData
#' \item Im = "NA", in experimentData
#' \item features_high, a vector of indicators, in featureData (0: No; 1: Yes; NA: not included in features_high)
#' \item features_all = "NA", in experimentData
#' \item threshold, estimated threshold, when threshold_fix, equals to threshold_start, in experimentData
#' }
#'
#' @export
#' @docType methods
#' @rdname fitNBth-methods
#' @examples
#'
#' library(Biobase)
#' library(dplyr)
#' data(demoData)
#' demoData <- fitPoisBG(demoData, size_scale = "sum")
#' demoData <- aggreprobe(demoData, use = "cor")
#' demoData <- BGScoreTest(demoData)
#' thmean <- 1 * mean(fData(demoData)$featfact, na.rm = TRUE)
#' demo_pos <- demoData[which(!fData(demoData)$CodeClass == "Negative"), ]
#' demo_neg <- demoData[which(fData(demoData)$CodeClass == "Negative"), ]
#' sc1_scores <- fData(demo_pos)[, "scores"]
#' names(sc1_scores) <- fData(demo_pos)[, "TargetName"]
#' features_high <- ((sc1_scores > quantile(sc1_scores, probs = 0.4)) &
#' (sc1_scores < quantile(sc1_scores, probs = 0.95))) |>
#' which() |>
#' names()
#' set.seed(123)
#' features_high <- sample(features_high, 100)
#' demoData <- fitNBth(demoData,
#' features_high = features_high,
#' sizefact_BG = demo_neg$sizefact,
#' threshold_start = thmean,
#' iterations = 5,
#' start_para = c(200, 1),
#' lower_sizefact = 0,
#' lower_threshold = 100,
#' tol = 1e-8)
#'
setGeneric("fitNBth",
signature = c("object"),
function(object, ...) standardGeneric("fitNBth")
)
#' @rdname fitNBth-methods
#' @aliases fitNBth,NanoStringGeoMxSet-method
setMethod(
"fitNBth", "NanoStringGeoMxSet",
function(object, split = TRUE,
features_high = NULL,
sizefact_BG = NULL, sizefact_start = sizefact_BG,
size_scale = c("sum", "first"),
threshold_start = NULL, threshold_fix = FALSE,
tol = 1e-7, iterations = 8,
start_para = c(threshold_start, 0.5),
lower_sizefact = 0, lower_threshold = threshold_start / 5) {
# check on tol
tol <- as.double(tol)
stopifnot(length(tol) == 1)
stopifnot(tol >= 0)
fDat <- Biobase::fData(object)
pDat <- Biobase::pData(object)
posdat <- object[-which(fDat$CodeClass == "Negative"), ]
countmat <- Biobase::exprs(posdat)
fDatNeg <- fDat[which(fDat$CodeClass == "Negative"), ]
# calculate probenum for the dataset
if ("probenum" %in% fvarLabels(posdat)) {
probenum <- fData(posdat)[["probenum"]]
} else {
stop("No `probenum` is found. Run `aggreprobe` first.")
}
names(probenum) <- rownames(fData(posdat))
# only calculate thmean if any of the two params are missing
if (any(c(is.null(sizefact_BG), is.null(threshold_start)))) {
if (isFALSE(split)) {
# single slide
if (!("sizefact" %in% varLabels(object))) {
stop("Please run `fitPoisBG` first.")
} else {
# calculate the thmean for WTA or CTA data
thmean <- mean(fDatNeg[["featfact"]])
}
} else {
# multiple slides
if (!("sizefact_sp" %in% varLabels(object))) {
stop("Please run `fitPoisBG` first with `groupvar`.")
} else {
# calculate the thmean for WTA or CTA data
thmean <- colMeans(fDatNeg[, grep("featfact_", fvarLabels(object))])[1]
}
}
}
# setting default value for sizefact_BG
if (is.null(sizefact_BG)) {
if (isFALSE(split)) {
# single slide
sizefact_BG <- pDat[["sizefact"]]
} else {
# multiple slides
sizefact_BG <- pDat[["sizefact_sp"]]
}
sizefact_start <- sizefact_BG
}
# setting default value for sizefact_start
if (is.null(threshold_start)) {
message(sprintf("`threshold_start` is missing. The default value is estimated based on fitPoisBG results with %s.",
ifelse(isTRUE(split), "multiple slides", "a single slide")))
thmean <- unname(thmean)
threshold_start <- thmean
}
# setting default value for features_high
if (is.null(features_high)) {
gene_sum <- rowSums(countmat)
if (any(grepl("WTA", toupper(Biobase::annotation(object))))) {
features_high <- names(which(((gene_sum > quantile(gene_sum, probs = 0.5)) & (gene_sum < quantile(gene_sum, probs = 0.95)))))
features_high <- sample(features_high, 1500)
} else if (any(grepl("CTA", toupper(Biobase::annotation(object))))) {
if ( !any(grepl("scores", colnames(fDat))) ) {
stop("Please run `BGScoreTest` first. If you run `BGScoreTest` before, please specify `split = TRUE` for multiple slides.")
} else {
if ( any(grepl("scores_", colnames(fDat))) ){
# fit the model with multiple slides
sc1_scores <- fData(posdat)[, grep("scores_", fvarLabels(posdat))]
rownames(sc1_scores) <- fData(posdat)[, "TargetName"]
features_high <- apply(sc1_scores, 2, function(x){
((x > quantile(x, probs = 0.4)) & (x < quantile(x, probs = 0.95)))
})
features_high <- names(which(apply(features_high, 1, all)))
} else {
sc1_scores <- fData(posdat)[, "scores"]
names(sc1_scores) <- fData(posdat)[, "TargetName"]
features_high <- ((sc1_scores > quantile(sc1_scores, probs = 0.4)) & (sc1_scores < quantile(sc1_scores, probs = 0.95)))
features_high <- names(which(features_high))
}
}
} else {
stop("No information is found to determine the data type (CTA or WTA).")
}
}
result <- fitNBth(
object = countmat[features_high, ],
probenum = probenum,
features_high = features_high,
sizefact_BG = sizefact_BG,
sizefact_start = sizefact_start,
size_scale = size_scale,
threshold_start = threshold_start,
threshold_fix = threshold_fix,
tol = tol,
iterations = iterations,
start_para = start_para,
lower_sizefact = lower_sizefact,
lower_threshold = lower_threshold
)
# update para0
Biobase::notes(object)$para0 <- ifelse(is.na(result$para0), "NA", result$para0)
# update para
Biobase::fData(object)[["para"]] <- matrix(NA,
nrow = nrow(object), ncol = 2,
dimnames = list(featureNames(object), c("signal", "r"))
)
Biobase::fData(object)[["para"]][colnames(result$para), ] <- t(result$para)
# update sizefact
object[["sizefact_fitNBth"]] <- result$sizefact
# update preci1
Biobase::notes(object)$preci1 <- ifelse(is.na(result$preci1), "NA", result$preci1)
# update conv0
Biobase::notes(object)$conv0 <- ifelse(is.na(result$conv0), "NA", result$conv0)
# update conv
Biobase::notes(object)$conv <- ifelse(is.na(result$conv), "NA", result$conv)
# update Im
Biobase::notes(object)$Im <- ifelse(is.na(result$Im), "NA", result$Im)
# update features_high
Biobase::fData(object)[["feature_high_fitNBth"]] <- 0
Biobase::fData(object)[["feature_high_fitNBth"]][match(result$features_high, Biobase::featureNames(object), nomatch = 0)] <- 1
# update features_all
Biobase::notes(object)$features_all <- ifelse(is.na(result$features_all), "NA", result$features_all)
# update threshold
Biobase::notes(object)$threshold <- ifelse(is.na(result$threshold), "NA", result$threshold)
return(object)
}
)
#' Negative Binomial threshold model
#'
#' Estimate the signal size factor for features above the background
#'
#' @param object count matrix with features in rows and samples in columns
#' @param probenum a vector of numbers of probes in each gene
#' @param features_high subset of features which are well above the background
#' @param sizefact_BG size factors for the background
#' @param sizefact_start initial value for size factors
#' @param size_scale method to scale the sizefact, sum(sizefact)=1 when size_scale="sum", sizefact[1]=1 when size_scale="first"
#' @param threshold_start initial value for threshold
#' @param threshold_fix whether to fix the threshold, default=FALSE
#' @param tol tolerance to determine convergence, default=1e-3
#' @param iterations maximum iterations to be run, default=5
#' @param start_para starting values for parameter estimation, default=c(threshold_start, 1)
#' @param lower_sizefact lower limit for sizefact, default=0
#' @param lower_threshold lower limit for threshold
#'
#' @return a list of following items, some items are place holders = NA
#' \itemize{
#' \item para0 = NA,
#' \item para, estimated parameters, "signal" "r" in rows and features in columns
#' \item sizefact, estimated size factor
#' \item preci1 = NA
#' \item conv0 = NA
#' \item conv = NA
#' \item Im = NA
#' \item features_high = features_high
#' \item features_all = NA
#' \item threshold, estimated threshold, when threshold_fix, equals to threshold_start
#' }
#'
#' @rdname fitNBth-methods
#' @aliases fitNBth,matrix-method
setMethod(
"fitNBth", "matrix",
function(object, features_high, probenum, sizefact_BG, sizefact_start = sizefact_BG, size_scale = c("sum", "first"), threshold_start, threshold_fix = FALSE, tol = 1e-7, iterations = 8,
start_para = c(threshold_start, 1), lower_sizefact = 0, lower_threshold = threshold_start / 5) {
size_scale <- match.arg(size_scale)
sizefact0 <- sizefact <- sizefact_start
threshold <- threshold_start
# mat <- matrix(1, nrow(object), 1)
if (is.null(names(probenum))) names(probenum) <- rownames(object)
for (iter in seq_len(iterations)) {
para <- NBth_paraopt(object[features_high, ], probenum[features_high], sizefact, sizefact_BG, threshold, start = start_para)
# result <- mleprobeNBall(object[,features_high], mat, sizefact0, sizefact,
# matrix(0,1,1), threshold, 0,
# c(rep(0,ncol(mat)), 1, threshold), 0)
features_NA <- features_high[unique(which(is.na(para), arr.ind = TRUE)[, 2])]
features_remain <- setdiff(features_high, features_NA)
for (i in seq_len(length(sizefact))) {
fun <- NBth_scalenll(object[features_remain, i], probenum[features_remain], t(para[1, features_remain]), t(para[2, features_remain]), sizefact_BG[i], threshold)
sizefact[i] <- optim(c(sizefact_start[i]), fun, lower = c(lower_sizefact), method = "L-BFGS-B")$par
}
if (size_scale == "first") {
scale_fac <- sizefact[1]
} else if (size_scale == "sum") {
scale_fac <- sum(sizefact)
}
sizefact <- sizefact / scale_fac
if (!threshold_fix) {
fun1 <- NBth_thnll(object[features_remain, ], probenum[features_remain], sizefact, sizefact_BG, scale_fac * t(para[1, features_remain]), t(para[2, features_remain]))
threshold <- optim(c(threshold_start), fun1, lower = c(lower_threshold), method = "L-BFGS-B")$par
}
message(sprintf("Iteration = %s, squared error = %s", iter, sum((sizefact - sizefact0)^2)))
if (sum((sizefact - sizefact0)^2) < tol) break
sizefact0 <- sizefact
}
message("Model converged.")
rownames(para) <- c("signal", "r")
return(list(
para0 = NA,
para = para,
sizefact = sizefact,
preci1 = NA,
conv0 = NA,
conv = NA,
Im = NA,
features_high = features_high,
features_all = NA,
threshold = threshold
))
}
)
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#' Negative Binomial threshold model
#'
#' Estimate the signal size factor for features above the background
#'
#' @param object a valid GeoMx S4 object
#' @param split indicator variable on whether it is for multiple slides (Yes, TRUE; No, FALSE)
#' @param features_high subset of features which are well above the background
#' @param sizefact_BG size factors for the background
#' @param sizefact_start initial value for size factors
#' @param size_scale method to scale the sizefact, sum(sizefact)=1 when size_scale="sum", sizefact[1]=1 when size_scale="first"
#' @param threshold_start initial value for threshold
#' @param threshold_fix whether to fix the threshold, default=FALSE
#' @param tol tolerance to determine convergence, default=1e-3
#' @param iterations maximum iterations to be run, default=5
#' @param start_para starting values for parameter estimation, default=c(threshold_start, 1)
#' @param lower_sizefact lower limit for sizefact, default=0
#' @param lower_threshold lower limit for threshold
#' @param ... additional argument list that might be used
#'
#' @importFrom Biobase pData
#' @importFrom Biobase fData
#' @importFrom Biobase exprs
#' @importFrom Biobase experimentData
#' @importFrom Biobase featureNames
#' @importFrom Biobase annotation
#'
#'
#' @return a valid GeoMx S4 object
#' \itemize{
#' \item para0 = "NA", in experimentData
#' \item para, estimated parameters, "signal" "r" in rows and features in columns, in featureData
#' \item sizefact, estimated size factor, in phenoData
#' \item preci1 = "NA", in experimentData
#' \item conv0 = "NA", in experimentData
#' \item conv = "NA", in experimentData
#' \item Im = "NA", in experimentData
#' \item features_high, a vector of indicators, in featureData (0: No; 1: Yes; NA: not included in features_high)
#' \item features_all = "NA", in experimentData
#' \item threshold, estimated threshold, when threshold_fix, equals to threshold_start, in experimentData
#' }
#'
#' @export
#' @docType methods
#' @rdname fitNBth-methods
#' @examples
#'
#' library(Biobase)
#' library(dplyr)
#' data(demoData)
#' demoData <- fitPoisBG(demoData, size_scale = "sum")
#' demoData <- aggreprobe(demoData, use = "cor")
#' demoData <- BGScoreTest(demoData)
#' thmean <- 1 * mean(fData(demoData)$featfact, na.rm = TRUE)
#' demo_pos <- demoData[which(!fData(demoData)$CodeClass == "Negative"), ]
#' demo_neg <- demoData[which(fData(demoData)$CodeClass == "Negative"), ]
#' sc1_scores <- fData(demo_pos)[, "scores"]
#' names(sc1_scores) <- fData(demo_pos)[, "TargetName"]
#' features_high <- ((sc1_scores > quantile(sc1_scores, probs = 0.4)) &
#' (sc1_scores < quantile(sc1_scores, probs = 0.95))) |>
#' which() |>
#' names()
#' set.seed(123)
#' features_high <- sample(features_high, 100)
#' demoData <- fitNBth(demoData,
#' features_high = features_high,
#' sizefact_BG = demo_neg$sizefact,
#' threshold_start = thmean,
#' iterations = 5,
#' start_para = c(200, 1),
#' lower_sizefact = 0,
#' lower_threshold = 100,
#' tol = 1e-8)
#'
setGeneric("fitNBth",
signature = c("object"),
function(object, ...) standardGeneric("fitNBth")
)
#' @rdname fitNBth-methods
#' @aliases fitNBth,NanoStringGeoMxSet-method
setMethod(
"fitNBth", "NanoStringGeoMxSet",
function(object, split = TRUE,
features_high = NULL,
sizefact_BG = NULL, sizefact_start = sizefact_BG,
size_scale = c("sum", "first"),
threshold_start = NULL, threshold_fix = FALSE,
tol = 1e-7, iterations = 8,
start_para = c(threshold_start, 0.5),
lower_sizefact = 0, lower_threshold = threshold_start / 5) {
# check on tol
tol <- as.double(tol)
stopifnot(length(tol) == 1)
stopifnot(tol >= 0)
fDat <- Biobase::fData(object)
pDat <- Biobase::pData(object)
posdat <- object[-which(fDat$CodeClass == "Negative"), ]
countmat <- Biobase::exprs(posdat)
fDatNeg <- fDat[which(fDat$CodeClass == "Negative"), ]
# calculate probenum for the dataset
if ("probenum" %in% fvarLabels(posdat)) {
probenum <- fData(posdat)[["probenum"]]
} else {
stop("No `probenum` is found. Run `aggreprobe` first.")
}
names(probenum) <- rownames(fData(posdat))
# only calculate thmean if any of the two params are missing
if (any(c(is.null(sizefact_BG), is.null(threshold_start)))) {
if (isFALSE(split)) {
# single slide
if (!("sizefact" %in% varLabels(object))) {
stop("Please run `fitPoisBG` first.")
} else {
# calculate the thmean for WTA or CTA data
thmean <- mean(fDatNeg[["featfact"]])
}
} else {
# multiple slides
if (!("sizefact_sp" %in% varLabels(object))) {
stop("Please run `fitPoisBG` first with `groupvar`.")
} else {
# calculate the thmean for WTA or CTA data
thmean <- colMeans(fDatNeg[, grep("featfact_", fvarLabels(object))])[1]
}
}
}
# setting default value for sizefact_BG
if (is.null(sizefact_BG)) {
if (isFALSE(split)) {
# single slide
sizefact_BG <- pDat[["sizefact"]]
} else {
# multiple slides
sizefact_BG <- pDat[["sizefact_sp"]]
}
sizefact_start <- sizefact_BG
}
# setting default value for sizefact_start
if (is.null(threshold_start)) {
message(sprintf("`threshold_start` is missing. The default value is estimated based on fitPoisBG results with %s.",
ifelse(isTRUE(split), "multiple slides", "a single slide")))
thmean <- unname(thmean)
threshold_start <- thmean
}
# setting default value for features_high
if (is.null(features_high)) {
gene_sum <- rowSums(countmat)
if (any(grepl("WTA", toupper(Biobase::annotation(object))))) {
features_high <- names(which(((gene_sum > quantile(gene_sum, probs = 0.5)) & (gene_sum < quantile(gene_sum, probs = 0.95)))))
features_high <- sample(features_high, 1500)
} else if (any(grepl("CTA", toupper(Biobase::annotation(object))))) {
if ( !any(grepl("scores", colnames(fDat))) ) {
stop("Please run `BGScoreTest` first. If you run `BGScoreTest` before, please specify `split = TRUE` for multiple slides.")
} else {
if ( any(grepl("scores_", colnames(fDat))) ){
# fit the model with multiple slides
sc1_scores <- fData(posdat)[, grep("scores_", fvarLabels(posdat))]
rownames(sc1_scores) <- fData(posdat)[, "TargetName"]
features_high <- apply(sc1_scores, 2, function(x){
((x > quantile(x, probs = 0.4)) & (x < quantile(x, probs = 0.95)))
})
features_high <- names(which(apply(features_high, 1, all)))
} else {
sc1_scores <- fData(posdat)[, "scores"]
names(sc1_scores) <- fData(posdat)[, "TargetName"]
features_high <- ((sc1_scores > quantile(sc1_scores, probs = 0.4)) & (sc1_scores < quantile(sc1_scores, probs = 0.95)))
features_high <- names(which(features_high))
}
}
} else {
stop("No information is found to determine the data type (CTA or WTA).")
}
}
result <- fitNBth(
object = countmat[features_high, ],
probenum = probenum,
features_high = features_high,
sizefact_BG = sizefact_BG,
sizefact_start = sizefact_start,
size_scale = size_scale,
threshold_start = threshold_start,
threshold_fix = threshold_fix,
tol = tol,
iterations = iterations,
start_para = start_para,
lower_sizefact = lower_sizefact,
lower_threshold = lower_threshold
)
# update para0
Biobase::notes(object)$para0 <- ifelse(is.na(result$para0), "NA", result$para0)
# update para
Biobase::fData(object)[["para"]] <- matrix(NA,
nrow = nrow(object), ncol = 2,
dimnames = list(featureNames(object), c("signal", "r"))
)
Biobase::fData(object)[["para"]][colnames(result$para), ] <- t(result$para)
# update sizefact
object[["sizefact_fitNBth"]] <- result$sizefact
# update preci1
Biobase::notes(object)$preci1 <- ifelse(is.na(result$preci1), "NA", result$preci1)
# update conv0
Biobase::notes(object)$conv0 <- ifelse(is.na(result$conv0), "NA", result$conv0)
# update conv
Biobase::notes(object)$conv <- ifelse(is.na(result$conv), "NA", result$conv)
# update Im
Biobase::notes(object)$Im <- ifelse(is.na(result$Im), "NA", result$Im)
# update features_high
Biobase::fData(object)[["feature_high_fitNBth"]] <- 0
Biobase::fData(object)[["feature_high_fitNBth"]][match(result$features_high, Biobase::featureNames(object), nomatch = 0)] <- 1
# update features_all
Biobase::notes(object)$features_all <- ifelse(is.na(result$features_all), "NA", result$features_all)
# update threshold
Biobase::notes(object)$threshold <- ifelse(is.na(result$threshold), "NA", result$threshold)
return(object)
}
)
#' Negative Binomial threshold model
#'
#' Estimate the signal size factor for features above the background
#'
#' @param object count matrix with features in rows and samples in columns
#' @param probenum a vector of numbers of probes in each gene
#' @param features_high subset of features which are well above the background
#' @param sizefact_BG size factors for the background
#' @param sizefact_start initial value for size factors
#' @param size_scale method to scale the sizefact, sum(sizefact)=1 when size_scale="sum", sizefact[1]=1 when size_scale="first"
#' @param threshold_start initial value for threshold
#' @param threshold_fix whether to fix the threshold, default=FALSE
#' @param tol tolerance to determine convergence, default=1e-3
#' @param iterations maximum iterations to be run, default=5
#' @param start_para starting values for parameter estimation, default=c(threshold_start, 1)
#' @param lower_sizefact lower limit for sizefact, default=0
#' @param lower_threshold lower limit for threshold
#'
#' @return a list of following items, some items are place holders = NA
#' \itemize{
#' \item para0 = NA,
#' \item para, estimated parameters, "signal" "r" in rows and features in columns
#' \item sizefact, estimated size factor
#' \item preci1 = NA
#' \item conv0 = NA
#' \item conv = NA
#' \item Im = NA
#' \item features_high = features_high
#' \item features_all = NA
#' \item threshold, estimated threshold, when threshold_fix, equals to threshold_start
#' }
#'
#' @rdname fitNBth-methods
#' @aliases fitNBth,matrix-method
setMethod(
"fitNBth", "matrix",
function(object, features_high, probenum, sizefact_BG, sizefact_start = sizefact_BG, size_scale = c("sum", "first"), threshold_start, threshold_fix = FALSE, tol = 1e-7, iterations = 8,
start_para = c(threshold_start, 1), lower_sizefact = 0, lower_threshold = threshold_start / 5) {
size_scale <- match.arg(size_scale)
sizefact0 <- sizefact <- sizefact_start
threshold <- threshold_start
# mat <- matrix(1, nrow(object), 1)
if (is.null(names(probenum))) names(probenum) <- rownames(object)
for (iter in seq_len(iterations)) {
para <- NBth_paraopt(object[features_high, ], probenum[features_high], sizefact, sizefact_BG, threshold, start = start_para)
# result <- mleprobeNBall(object[,features_high], mat, sizefact0, sizefact,
# matrix(0,1,1), threshold, 0,
# c(rep(0,ncol(mat)), 1, threshold), 0)
features_NA <- features_high[unique(which(is.na(para), arr.ind = TRUE)[, 2])]
features_remain <- setdiff(features_high, features_NA)
for (i in seq_len(length(sizefact))) {
fun <- NBth_scalenll(object[features_remain, i], probenum[features_remain], t(para[1, features_remain]), t(para[2, features_remain]), sizefact_BG[i], threshold)
sizefact[i] <- optim(c(sizefact_start[i]), fun, lower = c(lower_sizefact), method = "L-BFGS-B")$par
}
if (size_scale == "first") {
scale_fac <- sizefact[1]
} else if (size_scale == "sum") {
scale_fac <- sum(sizefact)
}
sizefact <- sizefact / scale_fac
if (!threshold_fix) {
fun1 <- NBth_thnll(object[features_remain, ], probenum[features_remain], sizefact, sizefact_BG, scale_fac * t(para[1, features_remain]), t(para[2, features_remain]))
threshold <- optim(c(threshold_start), fun1, lower = c(lower_threshold), method = "L-BFGS-B")$par
}
message(sprintf("Iteration = %s, squared error = %s", iter, sum((sizefact - sizefact0)^2)))
if (sum((sizefact - sizefact0)^2) < tol) break
sizefact0 <- sizefact
}
message("Model converged.")
rownames(para) <- c("signal", "r")
return(list(
para0 = NA,
para = para,
sizefact = sizefact,
preci1 = NA,
conv0 = NA,
conv = NA,
Im = NA,
features_high = features_high,
features_all = NA,
threshold = threshold
))
}
)
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