ArrayExpress (version 1.32.0)

processing-options: Functions to work with ArrayExpressHTS processing options

Description

Functions to get default ArrayExpressHTS processing options.

Usage

getDefaultFilteringOptions()
    getDefaultProcessingOptions()
    getDefaultRCloudOptions()

Arguments

Value

• 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<="" description="">
• duplicates
  "remove" by default, supported value: "keep", "remove"
• multihits
  "remove" by default, supported value: "keep", "remove"
• gapped
  "remove" by default, supported value: "keep", "remove"
• --- 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.
• --- 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.

See Also

getPipelineOptions, ArrayExpressHTS, ArrayExpressHTSFastQ

Examples

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