在r. 中运行rnorm创建数据帧时，数据帧出现错误

Question

我想计算df1 (class: data.frame):

中第一行与其余行之间的相关性

df1 <- data.frame(
Ensembl_ID = c("ENSG00000000003", "ENSG00000000005", "ENSG00000000419", 
"ENSG00000000457", "ENSG00000000460", "ENSG00000000938", 
"ENSG00000000971", "ENSG00000001036", "ENSG00000001084", 
"ENSG00000001167" ), 
`logFC 1` = c(-0.834165161710272, 1.02199443531549, 
-0.558658947885705, -0.390114219973209, -1.23551839713296, 
3.11429434221998, 0.283932163407262, -1.16908518620064, 
-0.597054772455507, -0.593624543273255), 
`logFC 2` = c(-1.18531035488942, 0.423719727339646, -1.23261719368372, 
0.0855281133529292, -1.52366830232278, 3.36692586561211, 
1.00323690950956, -0.000211248816114964, -4.74738483548391, 
-0.318176231083024), 
`logFC 3` = c(-0.262659255267546, 1.3962481061442, -0.548673555705647, 
-0.0149651083306594, -1.45458689193089, 2.54126941463459, 
1.17711308509307, -1.19425284921181, 1.17788731755683, 
-0.367897054652365 ), 
`logFC 4` = c(-0.840752912305256, 0.536548846040064, -0.277409459604357, 
-0.241073614962264, -0.875313153342293, 1.61789645804321, 
0.412287101096504, -1.11846661523232, -2.6274528854429, 
-0.760452698231182), 
`logFC 5` = c(-0.968784779247286, -0.502809694119192, -0.231526399163731, 
-0.530038395734114, -0.706006018337411, 3.58264357077653, 
-0.127521010699219, 0.270523387217103, 1.68335644352003, 
-0.314902131571829), 
`logFC 6` = c(-0.481754175843152, -0.440784040523259, -0.532975340622715, 
-0.182089795101371, -0.564807490336052, 1.74119896504534, 
-0.96169805631325, -0.721782763145306, -0.433459827401695, 
-0.727495835245995 ), 
`logFC 7` = c(-0.889343429110847, 1.07937149728343, -0.215144871523998, 
-0.92234350748557, -0.832108253417702, 2.02456082994848, 
-0.0434322861759954, -0.523126561938426, -0.556984056084809, 
-0.740331742513503), 
`logFC 8` = c(-0.858141567384178, 1.87728717064375, -0.381047638414538, 
-0.613568289061259, -1.92838339196505, 2.23393705735665, 
0.635389543483408, -0.466053620529111, -1.50483745357134, 
-1.33400859143521), 
`logFC 9` = c(-0.486388736112514, 0.789390852922639, -0.869434195504952, 
-0.70405854858187, -1.16488184095428, 2.91497178849082, 
-2.10331904053714, -0.571130459068143, -0.219526004620518, 
-0.301435496557957)
)

相关计算代码(我需要转置数据，因为cor函数要求列矩阵为x &y):

df2 <- cor(df1[1,],t(df1[2:10,]))

给出错误

Error in df1[2:10, ] : subscript out of bounds

然而，当我创建一个随机数据帧并运行相同的代码时，它工作得很好

# Creates a random matrix with 5 rows and 6 columns
mat=matrix(rnorm(30),5,6)
# Computes the correlation between the first row and the other 4 (cor function require transposed data)
cor(mat[1,],t(mat[2:5,]))

有人能帮我吗?请。欢迎提出任何建议。提前感谢

Answer 1

你可以改变一些事情。

1. cor需要数值数据，所以删除第一列。
2. 在本例中，mat[1,]是一个数值向量，对于df1，我们可以用unlist得到。

cor(unlist(df1[1,-1]),t(df1[2:10,-1]))
#         2      3      4      5      6      7      8     9   10
#[1,] 0.136 0.0787 0.0839 0.0911 -0.341 -0.326 -0.591 0.578 0.11

Answer 2

使用tidyverse

library(dplyr)
df1 %>% 
slice(1) %>% 
select(where(is.numeric)) %>% 
unlist %>%
cor(data.table::transpose(df1 %>%
slice(-1), make.names = 1) %>%
as.matrix)
ENSG00000000005 ENSG00000000419 ENSG00000000457 ENSG00000000460 ENSG00000000938 ENSG00000000971 ENSG00000001036 ENSG00000001084
[1,]       0.1360999      0.07867911      0.08393437      0.09114973       -0.341149      -0.3262614      -0.5907573       0.5779449
ENSG00000001167
[1,]       0.1100449