R: Creating a data frame from list with missing values. - r

Question

I have a list here that looks like this:
head(h)
[[1]]
[1] "gene=dnaA" "locus_tag=CD630_00010" "location=1..1320"
[[2]]
character(0)
[[3]]
[1] "locus_tag=CD630_05950" "location=719777..720313"
[[4]]
[1] "gene=dnrA" "locus_tag=CD630_00010" "location=50..1320"
I'm having trouble trying to manipulate this list to create a data.frame with three columns. For the rows with missing gene info, I want to list them as "gene=unnamed" and completely remove the empty rows into a matrix as shown:
[,1] [,2] [,3]
[1,] "gene=dnaA" "locus_tag=CD630_00010" "location=1..1320"
[2,] "gene=thrA" "locus_tag=CD630_05950" "location=719777..720313"
[3,] "gene=dnrA" "locus_tag=CD630_00010" "location=50..1320"
This is what I have right now, but I get an error about missing values in the gene column. Any suggestions?
h <- data.frame(h[lapply(h,length)>0])
h <- t(h)
rownames(h) <- NULL

Answer 1

# Data
l <- list(c("gene=dnaA","locus_tag=CD630_00010", "location=1..1320"),
character(0), c("locusc_tag=CD630_05950", "location=719777..720313"),
c("gene=dnrA","locus_tag=CD630_00010" ,"location=50..1320" ))
# Manipulation
n <- sapply(l, length)
seq.max <- seq_len(max(n))
df <- t(sapply(l, "[", i = seq.max))
df <- t(apply(df,1,function(x){
c(x[is.na(x)],x[!is.na(x)])}))
df <- df[rowSums(!is.na(df))>0, ]
df[is.na(df)] <- "gen=unnamed"
Output:
[,1] [,2] [,3]
[1,] "gene=dnaA" "locus_tag=CD630_00010" "location=1..1320"
[2,] "gen=unnamed" "locusc_tag=CD630_05950" "location=719777..720313"
[3,] "gene=dnrA" "locus_tag=CD630_00010" "location=50..1320"

Answer 2

There are a number of methods for binding lists with unequal lengths. See bind_rows from dplyr, rbind.fill from plyr or rbindlist from data.table. Here is using base R
## Sample data
h <- list(letters[1:3],
character(0),
letters[4:5])
out <- do.call(rbind, lapply(h, `length<-`, 3)) # fix lengths and make matrix
out <- out[rowSums(!is.na(out))>0, ] # remove empty rows
out[is.na(out)] <- "gen=unnamed" # rename NA
data.frame(out)
# X1 X2 X3
# 1 a b c
# 2 d e gen=unnamed