I have an excel file with the headings: trait, genotype_id, BLUE, BLUE_SE, BLUP, BLUP_SE and heritability.
All columns contain numbers except the trait column. This column has the traits Fe, Zn and S. So I have like 3 sets of data underneath each other. I want these to be summarised for the genotype so I have something like
genotype_id, BLUE_Fe, BLUE_Zn, BLUE_S, BLUE_SE_Fe etc.
How do I transform this file in R so that the traits are not only one column, but that I have the characteristics for Fe, Zn and S in separate columns respectively so that I can create a correlation matrix in R afterward?
I tried
data_wide <- spread(allBLUEs, trait, BLUE)
but this then obviously only moves the BLUEs into the same rows. I tried
data_wide <- spread(allBLUEs, key = trait, value = c(BLUE, BLUE_SE, BLUP, BLUP_SE, heritability), sep = "_")
but the value term seems to only be able to look at one column?
my data
df=tribble(~trait,~genotype_id,~BLUE,~BLUE_SE,~ BLUP,~BLUP_SE,~ heritability,
"Fe", 3, 47.2, 2.13, 43.0, 1.76, 0.685,
"Fe", 386, 42.5, 2.13, 39.8, 1.76, 0.685,
"Zn", 3, 24.4, 1.74, 23.6, 1.18, 0.456,
"S", 386, 1253, 51.3, 1269, 38.0, 0.545)
I think you can do it with pivot_wider
form tidyr
.
library(tibble)
library(tidyr)
df=tribble(~trait,~genotype_id,~BLUE,~BLUE_SE,~ BLUP,~BLUP_SE,~ heritability,
"Fe", 3, 47.2, 2.13, 43.0, 1.76, 0.685,
"Fe", 386, 42.5, 2.13, 39.8, 1.76, 0.685,
"Zn", 3, 24.4, 1.74, 23.6, 1.18, 0.456,
"S", 386, 1253, 51.3, 1269, 38.0, 0.545)
df %>%
pivot_wider(
names_from = trait,
values_from = BLUE:heritability
)
#> # A tibble: 2 × 16
#> genoty…¹ BLUE_Fe BLUE_Zn BLUE_S BLUE_…² BLUE_…³ BLUE_…⁴ BLUP_Fe BLUP_Zn BLUP_S
#> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 3 47.2 24.4 NA 2.13 1.74 NA 43 23.6 NA
#> 2 386 42.5 NA 1253 2.13 NA 51.3 39.8 NA 1269
#> # … with 6 more variables: BLUP_SE_Fe <dbl>, BLUP_SE_Zn <dbl>, BLUP_SE_S <dbl>,
#> # heritability_Fe <dbl>, heritability_Zn <dbl>, heritability_S <dbl>, and
#> # abbreviated variable names ¹genotype_id, ²BLUE_SE_Fe, ³BLUE_SE_Zn,
#> # ⁴BLUE_SE_S
Created on 2023-04-08 with reprex v2.0.2