How to calculate the correlation between lncRNA and gene expression
This article will explain in detail how to calculate the correlation between lncRNA and gene expression. The editor thinks it is very practical, so I share it with you as a reference. I hope you can get something after reading this article.
Calculate the correlation between lncRNA and gene expression
When constructing ceRNA network, it is necessary to calculate the expression correlation between lncRNA and protein coding gene (pc gene), and Pearson correlation coefficient is generally used. How to do it exactly?
1. First, get the expression matrix of lncRNA.
> head (lncRNA) lncRNA1 lncRNA2 lncRNA3 lncRNA4 lncRNA5sam1 7.80 5.81 6.40 6.11 4.87sam2 1.47 1.75 2.49 2.20 2.02sam3 0.00 1.28 0.00 0.00sam4 0.00 1.74 0.00 0.00sam5 1.83 0.99 0.72 0.69 0.50sam6 0.00 4.04 0.00 0.00 0.00 > dim (lncRNA) [1] 100 5
According to the expression data of lncRNA, it is the expression matrix of 5 lncRNA in 100 samples.
two。 Obtain the expression matrix of gene
> head (gene) gene 1 gene 2 gene 3 gene 4sam1 7.66 7.19 7.30 6.98sam2 1.34 0.29 1.77 1.61sam3 0.00 0.00 0.00sam4 0.14 0.41 0.56 0.77sam5 0.50 0.48 0.73 0.27sam6 0.00 0.00 0.00 > dim (gene) [1] 100 4
From the point of view of gene expression matrix, it is the expression matrix of 4 genes in 100 samples.
3. Calculate the expression correlation between lncRNA and gene.
# correlation calculation That's it > cor_matrix cor_matrix gene 1 gene 2 gene 3 gene 4lncRNA1 0.116393943 0.082464228 0.070419800 0.08509885lncRNA2-0.001455028-0.004848818 0.008653588-0.01047322lncRNA3 0.027655655 0.019760497 0.029196236 0.00464662lncRNA4-0.016414621-0.024633893-0.012498862-0.03835430lncRNA5-0.018116788-0.018668500-0.013198682-0.03287980 > pheatmap (cor_matrix) on "how to calculate lncRNA and That's all for the article "correlation of gene expression". Hope that the above content can be helpful to you, so that you can learn more knowledge, if you think the article is good, please share it for more people to see.
