fusions.process: LD-RTPCR fusion identification by Sanger
In MLPA: Multiplex Ligation-Dependent Probe Amplification Data Analysis

Description Usage Arguments Details Value Author(s) See Also

Automatically interpret gene fusions found by Sanger sequencing using the Ligation-Dependent PCR protocol.

1	fusions.process(input, design, sheet = NA, output = ".", cores = NA, ...)

`input`	Single character value, the path to the directory containing the AB1 files to process.
`design`	Data.frame describing all possible fusions (see Details).
`sheet`	Single character value, the name and path of a CSV file describing the files to process. 3 columns are expected: `ID` which gives a simpler sample name to use in outputs, `way` which defines if sequencing was 'forward' or 'reverse', and `file` which gives the file name and path relative to the `input` argument.
`output`	Single character value, the path to a directory in which to produce output files (will be created if doesn't yet exists).
`cores`	Single integer value, the amount of CPUs to use on the local machine to parallelize the computation. If `NA`, a guess will be made. If 1, computation will not use the `parallel` package at all but only loop over samples.
`...`	Further arguments are passed to `fusions.process.core`.

design must contain one row for each possible combination of a left primer with a right primer, whether this fusion is expected and relevant or not.

Expected columns in design are (excluding extra columns required with extra) :

left.name: Character, the name of the left primer.
left.seq: Character (uppercase), the sequence of the left primer (gene-specific part only).
left.unileft: Character (uppercase), the sequence of the left universal primer used for amplification.
left.symbol: Character, the symbol of the gene targeted by the left primer.
left.GRCh38: Character, the genomic coordinates of the last base of the left primer (chromosome:position:strand).
left.GRCh38_band: Character, the cytogenetic location of the gene targeted by the left primer.
right.name: Character, the name of the right primer.
right.seq: Character (uppercase), the sequence of the right primer (gene-specific part only).
right.uniright: Character (uppercase), the sequence of the right universal primer used for amplification.
right.symbol: Character, the symbol of the gene targeted by the right primer.
right.GRCh38: Character, the genomic coordinates of the last base of the right primer (chromosome:position:strand).
right.GRCh38_band: Character, the cytogenetic location of the gene targeted by the right primer.
seq_forward: Character (uppercase), the complete sequence expected in forward sequencing (concatenation of left.unileft, left.seq, right.seq, right.uniright and the right tail, if any).
seq_reverse: Character (uppercase), the complete sequence expected in reverse sequencing (reverse complement of a concatenation of the left tail, if any, left.unileft, left.seq, right.seq, right.uniright).

Please contact the authors to obtain a relevant design object.

Invisibly returns the aggregated table of top results for all samples.

Various files are produced, in location set by the output argument :

Top.csv: The aggregated table of top results for all samples.
*.pdf: One plot for each sample, showing the sequencing profile and the best alignments found.

Sylvain Mareschal

GEP.process

MLPA documentation built on May 2, 2020, 1:06 a.m.