Description Usage Arguments Details Value
View source: R/prepare.fastq.specification.R
Prepare FASTQ specification data frame to standardized format for downstream analyses.
1 2 3 | prepare.fastq.specification(sample.details, sample.id.column = 1,
fastq.columns = c(2, 3), patient.id.column = NA,
tissue.column = NA)
|
sample.details |
Data frame where each row represents a sample to be run. Must contain sample ID, path to tumour BAM, and path to normal BAM. |
sample.id.column |
Index or string giving column of |
fastq.columns |
Index or string giving column(s) of |
patient.id.column |
Index or string giving column of |
tissue.column |
Index or string giving column of |
This function prepares a data frame that can be used to run alignment. For paired-end reads, this data frame will contain three columns with names: sample.id, reads, mates For single-end reads, the data frame will contain two columns with names: sample.id, reads
Data frame with one row per sample to be run
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