Question: data prerprocessing coding
0
26 days ago by
sskimvd0
sskimvd0 wrote:

I have 200 columns and 80,000 rows of data.

Rows contain duplicate data.

I want to extract only the unique data from the duplicated data in the row, but leave only the maximum value in the column among the duplicated rows.

How can I do it?

thank you

sequencing snp R • 199 views
modified 13 days ago by rpolicastro3.2k • written 26 days ago by sskimvd0
2
13 days ago by
rpolicastro3.2k
Bloomington, IN
rpolicastro3.2k wrote:

Some example data. Note that I turned the rownames from your example into a column called 'rowid'.

before <- structure(list(rowid = c("r1", "r1", "r1", "r1", "r1", "r2",
"r2", "r2", "r2", "r2"), s1 = c(0L, 3L, 5L, 20L, 15L, 12L, 18L,
15L, 20L, 17L), s2 = c(16L, 13L, 11L, 1L, 18L, 20L, 0L, 3L, 7L,
4L), s3 = c(15L, 7L, 16L, 20L, 1L, 7L, 14L, 6L, 5L, 10L), s4 = c(14L,
10L, 5L, 7L, 18L, 14L, 20L, 1L, 10L, 12L), s5 = c(4L, 9L, 5L,
9L, 7L, 9L, 2L, 5L, 0L, 19L)), row.names = c(NA, -10L), class = c("tbl_df",
"tbl", "data.frame"))

> before
rowid s1 s2 s3 s4 s5
1     r1  0 16 15 14  4
2     r1  3 13  7 10  9
3     r1  5 11 16  5  5
4     r1 20  1 20  7  9
5     r1 15 18  1 18  7
6     r2 12 20  7 14  9
7     r2 18  0 14 20  2
8     r2 15  3  6  1  5
9     r2 20  7  5 10  0
10    r2 17  4 10 12 19

tidyverse solution

library("dplyr")

after <- before %>%
group_by(rowid) %>%
summarize(across(everything(), max))

> after
# A tibble: 2 x 6
rowid    s1    s2    s3    s4    s5
<chr> <int> <int> <int> <int> <int>
1 r1       20    18    20    18     9
2 r2       20    20    14    20    19

data.table solution. This will be quicker and more memory efficient if you have a lot of data and/or limited resources.

library("data.table")

setDT(before)
after <- before[, lapply(.SD, max), by=rowid]

> after
rowid s1 s2 s3 s4 s5
1:    r1 20 18 20 18  9
2:    r2 20 20 14 20 19
0
12 days ago by

with datamash:

input:

\$ cat file.txt

rowid   s1  s2  s3  s4  s5
r1  0   16  15  14  4
r1  3   13  7   10  9
r1  5   11  16  5   5
r1  20  1   20  7   9
r1  15  18  1   18  7
r2  12  20  7   14  9
r2  18  0   14  20  2
r2  15  3   6   1   5
r2  20  7   5   10  0
r2  17  4   10  12  19

output:

\$ datamash -sH -g1 max 2-6 < file.txt

GroupBy(rowid)  max(s1) max(s2) max(s3) max(s4) max(s5)
r1  20  18  20  18  9
r2  20  20  14  20  19