My data frame (DF1) looks like this :-
[Representative, DF1] [1]: https://i.stack.imgur.com/wZjzR.png
Doing the following for row 1 (MED1):
MED1 <- data_frame_merge[1,]
rownames(MED1) <- NULL
MED1 <- t(MED1)
MED1 <- as.data.frame(MED1)
MED1 <- tibble::rownames_to_column(MED1, "Fusion_Type")
MED1$Fusion_Type <- gsub("\\..*", "", MED1$Fusion_Type)
MED1$Fusion_Type <- as.factor(MED1$Fusion_Type)
names(MED1)[names(MED1) == "V1"] <- "TPM"
I get this:
[MED1, DF] [2]: https://i.stack.imgur.com/hhMf6.png
Basically, I am extracting first row from the 1st data frame and converting it into a data frame to look a certain way as (see image above).
My question is, how do I convert what I did with MED1 into a function so I can do this transformation for all rows I have in the first data frame.
I tried using for loops and functions several times but always run into errors.
I tried the code below but I am pretty sure its fraught with errors:
lsEOG<-list()
for (i in 1:nrow(df_main)) {
rownames(df)[i] <- df[i]
df[i] <- df[i]
rownames(df)[i] <- NULL
df[i] <- t(df[i])
df[i] <- as.data.frame(df[i])
df[i] <- tibble::rownames_to_column(df[i], "Fusion_Type")
df[i]$Fusion_Type <- gsub("\\..*", "", df[i]$Fusion_Type)
df[i]$Fusion_Type <- as.factor(df[i]$Fusion_Type)
names(df[i])[names(df[i]) == "V1"] <- "TPM"
lsEOG(df[i])<- df[i]
}
Error in rownames(df)[i] <- NULL : replacement has length zero (amongst many others)
Could you please help me fix it by turning the code into a function?
So that would be turning the below,
MED1 <- data_frame_merge[1,]
rownames(MED1) <- NULL
MED1 <- t(MED1)
MED1 <- as.data.frame(MED1)
MED1 <- tibble::rownames_to_column(MED1, "Fusion_Type")
MED1$Fusion_Type <- gsub("\\..*", "", MED1$Fusion_Type)
MED1$Fusion_Type <- as.factor(MED1$Fusion_Type)
names(MED1)[names(MED1) == "V1"] <- "TPM"
into a function? So it can be applied to all the rows of the data frame and outputs
CodePudding user response：
Try this:
library(tidyverse)
as_tibble(data_frame_merge,rownames = "MED") %>%
pivot_longer(cols = -MED, names_to = "Fusion_Type",values_to = "TMP") %>%
mutate(Fusion_Type = stringr::str_extract(Fusion_Type, "(?<=\\d_).*$"))
Output:
# A tibble: 28 × 3
MED Fusion_Type TMP
<chr> <chr> <dbl>
1 MED1 PML_RARA 57.5
2 MED1 PML_RARA 178.
3 MED1 PML_RARA 20.6
4 MED1 PML_RARA 139.
5 MED10 PML_RARA 158.
6 MED10 PML_RARA 110.
7 MED10 PML_RARA 180.
8 MED10 PML_RARA 128.
9 MED11 PML_RARA 81.8
10 MED11 PML_RARA 91.3
# … with 18 more rows
Input:
data_frame_merge = structure(list(`TCGA-AB-2991_PML_RARA` = c(57.5155040249228,
157.661027088761, 81.79538436234, 176.603480800986, 188.093456858769,
9.11129987798631, 105.621097609401), `TCGA-AB-3012_PML_RARA` = c(178.483808878809,
110.287002893165, 91.3229470606893, 191.366669069976, 90.6668312381953,
135.514127090573, 114.526680391282), `TCGA-AB-2872_PML_RARA` = c(20.5849365331233,
179.964994080365, 49.217546870932, 8.41190670616925, 65.5841438565403,
190.900729829445, 177.907863212749), `TCGA-AB-2999_PML_RARA` = c(138.56068123132,
128.101362753659, 198.853955324739, 131.141159823164, 141.706093633547,
108.813204942271, 118.828404089436)), class = "data.frame", row.names = c("MED1",
"MED10", "MED11", "MED12", "MED12L", "MED13", "MED13L"))
data_frame_merge looks like this:
TCGA-AB-2991_PML_RARA TCGA-AB-3012_PML_RARA TCGA-AB-2872_PML_RARA TCGA-AB-2999_PML_RARA
MED1 57.51550 178.48381 20.584937 138.5607
MED10 157.66103 110.28700 179.964994 128.1014
MED11 81.79538 91.32295 49.217547 198.8540
MED12 176.60348 191.36667 8.411907 131.1412
MED12L 188.09346 90.66683 65.584144 141.7061
MED13 9.11130 135.51413 190.900730 108.8132
MED13L 105.62110 114.52668 177.907863 118.8284