This function takes sequencing results in wide format and converts them into a long format data frame. It extracts sample names from column names, processes each sample separately, and then binds them together. Finally, it renames and reorders columns to match the desired output format.
Value
A data frame in long format with columns "chr", "from", "to",
"ref", "alt", "NV", "DP", "VAF", and "sample_name".
Examples
# Example data frame in wide format
seq_results <- data.frame(chr = c("chr1", "chr2"),
chr_pos = c(100, 200),
ref = c("A", "C"),
alt = c("T", "G"),
causes = c("SBS5", "SBS1"),
classes = c("germinal", "passneger"),
Sample.A.occurrences = c(10, 90),
Sample.A.coverage = c(100, 100),
Sample.A.VAF = c(0.1, 0.9),
normal_sample.occurrences = c(45, 52),
normal_sample.coverage = c(100, 100),
normal_sample.VAF = c(0.45, 0.52))
seq_results
#> chr chr_pos ref alt causes classes Sample.A.occurrences Sample.A.coverage
#> 1 chr1 100 A T SBS5 germinal 10 100
#> 2 chr2 200 C G SBS1 passneger 90 100
#> Sample.A.VAF normal_sample.occurrences normal_sample.coverage
#> 1 0.1 45 100
#> 2 0.9 52 100
#> normal_sample.VAF
#> 1 0.45
#> 2 0.52
# Convert to long format
seq_to_long(seq_results)
#> chr from ref alt causes classes NV DP VAF sample_name to
#> 1 chr1 100 A T SBS5 germinal 10 100 0.10 Sample.A 100
#> 2 chr2 200 C G SBS1 passneger 90 100 0.90 Sample.A 200
#> 3 chr1 100 A T SBS5 germinal 45 100 0.45 normal_sample 100
#> 4 chr2 200 C G SBS1 passneger 52 100 0.52 normal_sample 200