comparison edger.R @ 17:fb9dc2ee2fd4 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212

16:ae2aad0a6d50

    # Split up contrasts separated by comma into a vector then sanitise
    contrast_data <- unlist(strsplit(opt$contrastData, split = ","))
}
contrast_data <- sanitise_equation(contrast_data)
contrast_data <- gsub(" ", ".", contrast_data, fixed = TRUE)

bcv_pdf <- make_out("bcvplot.pdf")
bcv_png <- make_out("bcvplot.png")
ql_pdf <- make_out("qlplot.pdf")
ql_png <- make_out("qlplot.png")

design <- model.matrix(formula, factors)

for (i in seq_along(factor_list)) {
    colnames(design) <- gsub(factor_list[i], "", colnames(design), fixed = TRUE)
}

# Calculating normalising factor, estimating dispersion
data <- calcNormFactors(data, method = opt$normOpt)

if (want_robust) {

17:fb9dc2ee2fd4

    # Split up contrasts separated by comma into a vector then sanitise
    contrast_data <- unlist(strsplit(opt$contrastData, split = ","))
}
contrast_data <- sanitise_equation(contrast_data)
contrast_data <- gsub(" ", ".", contrast_data, fixed = TRUE)
# Convert colons to dots to match design matrix column name processing
contrast_data <- gsub(":", ".", contrast_data, fixed = TRUE)

bcv_pdf <- make_out("bcvplot.pdf")
bcv_png <- make_out("bcvplot.png")
ql_pdf <- make_out("qlplot.pdf")
ql_png <- make_out("qlplot.png")

design <- model.matrix(formula, factors)

for (i in seq_along(factor_list)) {
    colnames(design) <- gsub(factor_list[i], "", colnames(design), fixed = TRUE)
}

# Ensure column names are syntactically valid
colnames(design) <- make.names(colnames(design))

# Calculating normalising factor, estimating dispersion
data <- calcNormFactors(data, method = opt$normOpt)

if (want_robust) {