匹配相关矩阵的行名和列名

Question

I have a vector with 3990 names (these are the column names of my dataframe) and I want to match them with the rows of my data. My data contains correlation values and I want to subset my data based on the matches found

My data looks like this:

I tried using grepl

result <- filter(df, grepl(paste(column_names, collapse="|"), rownames(df)))

but I get an error

error in 'grepl()': ! invalid regular expression

my expected output would be

does anyone have any suggestions on how can this be done?

would really be great if someone could help me with this!

Best, Shweta

Answer 1

Try this:

library(dplyr)
dat %>%
  filter(grepl(paste0("\\b", names(.), "\\b", collapse="|"), rownames(dat)))
          TATA TATB TATC TATD
TATA,TATA  0.8  0.2  0.5  0.1
TATB       0.2  0.9  0.4  0.5
TATA       0.9  0.4  0.2  0.1

Data:

dat <- data.frame(TATA = c(0.8,0.2,0.1,0.01,0.9),
                  TATB = c(0.2,0.9,0.2,0.4,0.4),
                  TATC = c(0.5,0.4,0.3,0.3,0.2),
                  TATD = c(0.1,0.5,0.15,0.5,0.1),
                  row.names = c("TATA,TATA", "TATB", "TATE", "TATM", "TATA"))

Answer 2

Three options you can try:

library(reshape2)
melt(as.matrix(dat)

data.frame(rows=rownames(dat)[row(dat)], vars=colnames(dat)[col(dat)], values=c(dat))

as.data.frame(as.table(as.matrix(dat)))

result:

        Var1 Var2        Freq
1  TATA,TATA TATA 0.872624483
2       TATB TATA 0.533790730
3       TATE TATA 0.110495616
4       TATM TATA 0.253893718
5       TATA TATA 0.303576730
6  TATA,TATA TATB 0.774815753
7       TATB TATB 0.941361633
8       TATE TATB 0.305219935
9       TATM TATB 0.101124692
10      TATA TATB 0.968514156
11 TATA,TATA TATC 0.891697937
12      TATB TATC 0.006223573
13      TATE TATC 0.045138657
14      TATM TATC 0.848485971
15      TATA TATC 0.995542845
16 TATA,TATA TATD 0.479559761
17      TATB TATD 0.981808763
18      TATE TATD 0.227518091
19      TATM TATD 0.767491049
20      TATA TATD 0.410935185

data:

dat <- data.frame(TATA = runif(5),
                  TATB = runif(5),
                  TATC = runif(5),
                  TATD = runif(5),
                  row.names = c("TATA,TATA", "TATB", "TATE", "TATM", "TATA"))

EDIT:

Using regex matching to subset your input data, as a first step:

cols <- grep(pattern = paste0(rownames(dat), collapse = "|"), x = colnames(dat), value = TRUE)
rows <- grep(pattern = paste0(colnames(dat), collapse = "|"), x = rownames(dat), value = TRUE)

dat2 <- dat[rownames(dat) %in% rows, colnames(dat) %in% cols]

Yielding:

as.data.frame(as.table(as.matrix(dat2)))
       Var1 Var2      Freq
1 TATA,TATA TATA 0.6908219
2      TATB TATA 0.7255142
3      TATA TATA 0.1022963
4 TATA,TATA TATB 0.7291625
5      TATB TATB 0.7420069
6      TATA TATB 0.7480157