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relative_abundance_limma.r
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# if (!requireNamespace("BiocManager", quietly = TRUE))
# install.packages("BiocManager")
#
# BiocManager::install("limma")
#input = "HDAC"
#input = "HDAC_norm"
#input = "BCC_453"
input = "BCC_468"
if(input=="HDAC"){
infile_name = '/home/sander/Documents/LabFBT/Colleague_work/180306_LdC_SWATH/Relative_abundance/190129_HDAC_BCS_SWATHpaper/190130_HDAC_RA_SW.csv'
outfile_name = '/home/sander/Documents/LabFBT/Colleague_work/180306_LdC_SWATH/Relative_abundance/190129_HDAC_BCS_SWATHpaper/190130_HDAC_RA_SW_limma.csv'
all_contrasts = list(
"Time1-Time2",
"Time1-Time3",
"Time1-Time4",
"Time1-Time5",
"Time1-Time6",
"Time1-Time7",
"Time1-Time8",
"Time1-Time9",
"Time2-Time3",
"Time2-Time4",
"Time2-Time5",
"Time2-Time6",
"Time2-Time7",
"Time2-Time8",
"Time2-Time9",
"Time3-Time4",
"Time3-Time5",
"Time3-Time6",
"Time3-Time7",
"Time3-Time8",
"Time3-Time9",
"Time4-Time5",
"Time4-Time6",
"Time4-Time7",
"Time4-Time8",
"Time4-Time9",
"Time5-Time6",
"Time5-Time7",
"Time5-Time8",
"Time5-Time9",
"Time6-Time7",
"Time6-Time8",
"Time6-Time9",
"Time7-Time8",
"Time7-Time9",
"Time8-Time9"
)
}
if(input=="HDAC_norm"){
infile_name = '/home/sander/Documents/LabFBT/Colleague_work/180306_LdC_SWATH/Relative_abundance/190129_HDAC_BCS_SWATHpaper/181212_HDAC_norm_parse_edit_RA_forStats_SW.csv'
outfile_name = '/home/sander/Documents/LabFBT/Colleague_work/180306_LdC_SWATH/Relative_abundance/190129_HDAC_BCS_SWATHpaper/181212_HDAC_norm_parse_edit_RA_forStats_SW_limma.csv'
all_contrasts = list(
"Time1-Time2",
"Time1-Time3",
"Time1-Time4",
"Time1-Time5",
"Time1-Time6",
"Time1-Time7",
"Time1-Time8",
"Time1-Time9",
"Time2-Time3",
"Time2-Time4",
"Time2-Time5",
"Time2-Time6",
"Time2-Time7",
"Time2-Time8",
"Time2-Time9",
"Time3-Time4",
"Time3-Time5",
"Time3-Time6",
"Time3-Time7",
"Time3-Time8",
"Time3-Time9",
"Time4-Time5",
"Time4-Time6",
"Time4-Time7",
"Time4-Time8",
"Time4-Time9",
"Time5-Time6",
"Time5-Time7",
"Time5-Time8",
"Time5-Time9",
"Time6-Time7",
"Time6-Time8",
"Time6-Time9",
"Time7-Time8",
"Time7-Time9",
"Time8-Time9"
)
}
if(input=="BCC_453"){
infile_name = '/home/sander/Documents/LabFBT/Colleague_work/180306_LdC_SWATH/Relative_abundance/190129_HDAC_BCS_SWATHpaper/181211_BCC_Norm_parse_edit_RA_forStats_453_SW.csv'
outfile_name = '/home/sander/Documents/LabFBT/Colleague_work/180306_LdC_SWATH/Relative_abundance/190129_HDAC_BCS_SWATHpaper/181211_BCC_Norm_parse_edit_RA_forStats_453_SW_limma.csv'
all_contrasts = list(
"Time1-Time2",
"Time1-Time3",
"Time2-Time3"
)
}
if(input=="BCC_468"){
infile_name = '/home/sander/Documents/LabFBT/Colleague_work/180306_LdC_SWATH/Relative_abundance/190129_HDAC_BCS_SWATHpaper/181211_BCC_Norm_parse_edit_RA_forStats_468_SW.csv'
outfile_name = '/home/sander/Documents/LabFBT/Colleague_work/180306_LdC_SWATH/Relative_abundance/190129_HDAC_BCS_SWATHpaper/181211_BCC_Norm_parse_edit_RA_forStats_468_SW_limma.csv'
all_contrasts = list(
"Time1-Time2",
"Time1-Time3",
"Time2-Time3"
)
}
dataset = read.csv(
infile_name,
header=TRUE,
stringsAsFactors=FALSE,
sep=";"
)
write.table(t(colnames(dataset[2:dim(dataset)[2]])), outfile_name, sep=",", col.names=FALSE)
library(limma)
# transpose of dataset
dataset_t <- t(dataset)
colnames(dataset_t) <- dataset_t[1, ]
dataset_t <- dataset_t[-1, ]
# Create design matrix
target <- data.frame(Time = colnames(dataset_t))
target$Time <- as.factor(target$Time)
design <- model.matrix(~ 0+ Time, data = target)
# Fit full model
fit <- lmFit(dataset_t, design = design)
# Look at contrasts
for(current_contrast in all_contrasts){
write.table(current_contrast, outfile_name, sep=",", append=TRUE, col.names = FALSE, row.names=FALSE)
contrast <- makeContrasts(current_contrast, levels = design)
fit2 <- contrasts.fit(fit, contrast)
fit2 <- eBayes(fit2)
z = topTable(fit2, adjust="BH", number = Inf, sort.by = "none")
write.table(t(z), outfile_name, sep=",", append=TRUE, col.names=FALSE)
}