[英]R cor across rows and columns
Hello I currently have a matrix that has genes as row.name and Tissue Type as colnames. 您好,我目前有一个矩阵,其基因为row.name,组织类型为colnames。 If I:
如果我:
> cor(matrix)
> str(DataCor2)
num [1:39453, 1:19] 0.502 7.974 33.462 0 14.543 ...
- attr(*, "dimnames")=List of 2
..$ : chr [1:39453] "AC205376.4_FG003" "GRMZM2G024563" ...
..$ : chr [1:19] "V18_Meotic_TasselR1" "V18_Meotic_TasselR2" ...
I get a correlation between tissue types. 我得到了组织类型之间的关联。 What I want to do is get a correlation of a subsets of genes across each tissue type for a heat map, I tried:
我想做的是获取每种组织类型的基因子集与热图的相关性,我尝试过:
cor(v, t(v)) cor(v,t(v))
But I get an error saying incompatible dimensions. 但是我收到一个错误的消息,说尺寸不兼容。 Here is part of the data and I want to see a correlation of expression levels between genes across tissue types.
这是数据的一部分,我希望了解各种组织类型之间基因之间表达水平的相关性。 The heat map would look similar to the matrix with genes on the Y axis and tissue on the X axis.
热图看起来类似于在Y轴上有基因,在X轴上有组织的矩阵。 Hopefully it makes more sense.
希望它更有意义。
Suppose you want to subset
the genes
based on the prefix
and do the cor
on each subset
假设你要
subset
的genes
基础上的prefix
并做cor
上的每个subset
res <- lapply(split(1:nrow(mat1), gsub("_.*", "", rownames(mat1))),
function(i) cor(mat1[i,]))
set.seed(29)
mat1 <- matrix(sample(0:80, 15*3, replace=TRUE), ncol=3,
dimnames=list(paste(rep(c('V18', 'V19'), c(8,7)), LETTERS[1:15],
sep="_"), paste0("AC", 1:3)))
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