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jeffreypullin/mass-spec.R

Created April 9, 2024 10:02
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mass-spec.R
# BiocManager::install("edgeR")
library(edgeR)
library(readr)
library(janitor)
library(dplyr)
data <- read_delim(
"~/Downloads/270324_DRIX082_pg.matrix.tsv",
name_repair = make_clean_names,
show_col_types = FALSE
)
mat <- data |>
select(c(7, 10, 11)) |>
as.matrix()
colnames(mat) <- c("HC2", "PD2", "PD8")
rownames(mat) <- data$genes
fit <- lmFit(mat, design=c(1,-1,-1))
fit <- eBayes(fit)
topTable(fit, number = 10, sort.by = "t")
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