processing-options: Functions to work with ArrayExpressHTS processing options
In ArrayExpressHTS: ArrayExpress High Throughput Sequencing Processing Pipeline

Description Usage Arguments Value Author(s) See Also Examples

Functions to get default ArrayExpressHTS processing options.

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    getDefaultFilteringOptions()
    getDefaultProcessingOptions()
    getDefaultRCloudOptions()

No arguments.

These functions return default options used for ArrayExpressHTS processing.

Function getDefaultFilteringOptions returns a list of filtering options. These options control filtering of BAM files after alignemnt.

`mismatches`	`2` by default, number of mismatches
`chr_ignore`	`c("MT")` by default, reference names to ignore
`minqual`	`10` by default
`minmapq`	`1` by default
`maxN`	`2` by default
`maxpol`	`0.75` by default, ither a proportion (<0) or an integer
`duplicates`	`"remove"` by default, supported value: `"keep"`, `"remove"`
`multihits`	`"remove"` by default, supported value: `"keep"`, `"remove"`
`gapped`	`"remove"` by default, supported value: `"keep"`, `"remove"`

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Function getDefaultProcessingOptions returns a list of options used throught the processing. These options control alignment and counting.

These options include:

`stranded`	`FALSE` by default, set to `TRUE` if a strand specific protocol was used
`insize`	`NULL` by default, the insert size, an integer, which will be automatically determined if set to `NULL`
`insizedev`	`NULL` by default, insert size deviation, an integer, which will be automatically determined if set to `NULL`
`reference`	`"genome"` by default, controlls whether alignment is performed using `"genome"` or `"transcriptome"` reference.
`aligner`	`"tophat"` by default, supported values are: `"tophat"`, `"bowtie"`, `"bwa"` or `"custom"`
`aligner_options`	`NULL` by default, string of options to be passed to the aligner according to manual.
`count_feature`	`"transcript"` by default, count over `"gene"` or `"transcript"`
`count_method`	`"cufflinks"` by default, supported: `"cufflinks"`, `"mmseq"` or `"count"`
`count_options`	options for count software
`standardise`	`FALSE` by default, supported: `TRUE`, `FALSE`
`normalisation`	`"rpkm"` by default, supported: `"none"` or `"rpkm"`
`filter`	`"TRUE"` by defult, supported: `"TRUE"`, `"FALSE"`
`filtering_options`	these are the default filtering options, see above.

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Function getDefaultRCloudOptions returns a set of R Cloud options related to R Cloud resources and execution flow.

These include:

`nnodes`	`"automatic"` by default, supported: `"automatic"` or a numeric value, e.g. `10`
`pool`	`"32G"` by default, supported: `"4G"`, `"8G"`, `"16G"`, `"32G"`, `"64G"`
`nretries`	`4` by default, a numberic value.

Andrew Tikhonov <andrew@ebi.ac.uk>, Angela Goncalves <angela.goncalves@ebi.ac.uk>

getPipelineOptions, ArrayExpressHTS, ArrayExpressHTSFastQ

    
    # get filtering options
    getDefaultFilteringOptions()
    
    # get alignment and counting options
    getDefaultProcessingOptions()
    
    # get R Cloud options
    getDefaultRCloudOptions()