r - .I want to do a pairwise.t.test of every column against every column in a dataframe

Question

violin plots generated from data frame The numbers in each column represent localisation of signal relative to another signal inside nuclei of cells. There are 3 treatment conditions and 7 time points of treatment + 2 controls giving a total of 23 columns (see violin plots). I would like to perform a t-test or a Wilcox t-test with each column to each column. I think I have done it before with a pairwise.t.test(Chr). However, the function requires to define how you group your data and I would like to group mine by columns. I've imported my data:

Chr <- read_csv("Chromocenters-intensity.csv", 
+     na = "NA")

Parsed with column specification: cols( .default = col_double() )

Imported dataset into R

And then tried:

 pairwise.t.test(Chr, cols())

Error in order(y) : unimplemented type 'list' in 'orderVector1'

pairwise.wilcox.test(Chr,g=cols(Chr))

Error: Some col_types are not S3 collector objects: 1

I do not understand what the errors mean.

a normal t.test works fine:

t.test(Chr$S0,Chr$S1)

Welch Two Sample t-test

data: Chr$S0 and Chr$S1 t = 0.85955, df = 154.12, p-value = 0.3914 alternative hypothesis: true difference in means is not equal to 0 95 percent confidence interval: -1.920629 4.879370 sample estimates: mean of x mean of y 100.41579 98.93642

but how do I scale it up to include every column by every column?

Thank you

标签： rt-testpairwise

Answer 1

您可以使用expand.grid和apply。

data <- as.data.frame(sapply(1:23,function(x){runif(470,1,200)}))
names(data) <-c(paste0("S",0:7),paste0("N",1:7),paste0("P",1:7),"TKO")
pairs <- expand.grid(names(data),names(data))
result <- data.frame(pairs,p.val = apply(pairs,1,function(x){t.test(data[x[1]],data[x[2]])$p.val}))
result
    Var1 Var2          p.val
1     S0   S0 1.000000000000
2     S1   S0 0.573722556263
3     S2   S0 0.874552764274
4     S3   S0 0.467670724537
5     S4   S0 0.700539636188
6     S5   S0 0.736422364244
7     S6   S0 0.599066387580
8     S7   S0 0.940641228509
9     N1   S0 0.727290760056
10    N2   S0 0.057120608982
11    N3   S0 0.523554180769
12    N4   S0 0.485633891380

不要忘记稍后更正以进行多次测试。