processing-options: Functions to work with ArrayExpressHTS processing options

In andrewtikhonov/ArrayExpressHTS: ArrayExpress High Throughput Sequencing Processing Pipeline

Description

Functions to get default ArrayExpressHTS processing options.

Usage

    getDefaultFilteringOptions()
    getDefaultProcessingOptions()
    getDefaultRCloudOptions()

Arguments

No 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
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.

Author(s)

Andrew Tikhonov <[e-mail]>, Angela Goncalves <[e-mail]>

See Also

getPipelineOptions, ArrayExpressHTS, ArrayExpressHTSFastQ

Examples

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

andrewtikhonov/ArrayExpressHTS documentation built on May 28, 2019, 4:57 p.m.