Error in transforming blank spaces into 0 after pivoting_wider for performing DGEList function in R

Question

the df I'm working on originally is a long format table like below:-

VALUE	Gene_Symbol	Sample_ID
12253	BRCA	P1
42356	CAMP	P2

Then for generating the DGEList, I decided to transform it into a wide format and generated below table:

	P1	P2	P3	P4
null	2423	46456	74564	523424
CAMP		42356
BRCA	12253		453	658665

because some samples may not express a certain gene, hence the console leave it blank when I wide pivot it. When I view() the df, it showed as blank. But when I do summery() it shows as NULL in the console.

Right now, I am trying to use apply() to replace the blank with 0 but with no luck, all values turned into 0.

Answer 1

The values_fill function in tidy::pivot_wider should do the trick:

tidyr::pivot_wider(df, 
                     names_from = Sample_ID, 
                     values_from = VALUE, 
                     values_fill = 0)

Output:

#   Gene_Symbol    P1    P2
#   <chr>       <int> <int>
# 1 BRCA        12253     0
# 2 CAMP            0 42356

Data

df <- read.table(text = "VALUE  Gene_Symbol Sample_ID
12253   BRCA    P1
42356   CAMP    P2
", h = T)

Generally, you could replace the values of NA in a data frame without apply using something like this:

df_na <- tidyr::pivot_wider(df, names_from = Sample_ID, values_from = VALUE)

#   Gene_Symbol    P1    P2
#   <chr>       <int> <int>
# 1 BRCA        12253    NA
# 2 CAMP           NA 42356

df_na[is.na(df_na)] <- 0

#   Gene_Symbol    P1    P2
#   <chr>       <int> <int>
# 1 BRCA        12253     0
# 2 CAMP            0 42356