Hello,
I have Chip-Seq data for two transcription factor (TF1,TF2) and they have significant numbers of peaks overlapped (MACS2 Peak calling) and I want to plot linear correlation between the signal of TF1 and TF2 peaks in the shared binding sites. Please guide me. Thank you
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qudrat.nii •
You can do something like this for your shared binding site in R.
library(ggplot2)
#Creating data for your TF signals
TF1_S <- c(3.2, 4.5, 5.6, 2.1, 6.7)
TF2_S <- c(2.8, 3.9, 5.0, 1.8, 6.2)
#Create dataframe
data <- data.frame(TF1 = TF1_S, TF2 = TF2_S)
#Calculate Correlation using `cor()` function
correlation_coefficient <- cor(data$TF1, data$TF2)
#Plot correlation Scaterplot in ggplot2
ggplot(data, aes(x = TF1, y = TF2)) + geom_point() +
labs(title = "Linear Correlation between TF1 and TF2 Peaks",
x = "TF1 Signal", y = "TF2 Signal") +
geom_smooth(method = "lm", se = FALSE, color = "red") +
geom_text(x = min(data$TF1), y = max(data$TF2), label = paste("Correlation:", round(correlation_coefficient, 2)))
Where do you get TF signals from? I have bigwig file for TFs. How to get signal from these files?
I made mock signals for illustration purpose. Please check the link below for how to get signals from your bigwig files-
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