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Merge with the original data.frame with information about the disease.

Barcelona/R/modelling.R

Lines 53 to 56 in f54750b

# TODO: Merge with the original data.frame with information about the disease.
models2 <- list(model1, model1i, model2, model2i)
Ab <- lapply(A, function(x) scale2(x, bias = TRUE)/sqrt(NCOL(x)))
out <- lapply(models2, use, A = Ab2, c1 = shrinkage[1:2])

This issue was generated by todo based on a TODO comment in f54750b. It's been assigned to @llrs because they committed the code.

See if this is a good choice

Barcelona/R/diversity.R

Lines 47 to 52 in a2242f4

# conn <- gzfile("data/TNF.all.samples.original.counts.tsv.gz") # TODO See if this is a good choice
rna <- read.table(conn, sep = "\t", check.names = FALSE)
colnames(rna) <- gsub(" reseq$", "", colnames(rna))
colnames(rna)[grep("[Ww]", colnames(rna))] <- tolower(colnames(rna)[grep("[Ww]", colnames(rna))])

This issue was generated by todo based on a TODO comment in a2242f4. It's been assigned to @llrs because they committed the code.

study as cofacto

Barcelona/R/QC.R

Lines 156 to 161 in 6426500

# TODO study as cofacto
library("decontam")
count_decontam <- t(as.matrix(counts))
colnames(count_decontam) <- family$Family
decontamination <- isContaminant(count_decontam, neg = out$Study %in% "NC",
method = "auto", conc = out$Concentr,

This issue was generated by todo based on a TODO comment in 6426500. It's been assigned to @llrs because they committed the code.

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