processing-options: Functions to work with ArrayExpressHTS processing options

Description Usage Arguments Value Author(s) See Also Examples

Description

Functions to get default ArrayExpressHTS processing options.

Usage

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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 <[email protected]>, Angela Goncalves <[email protected]>

See Also

getPipelineOptions, ArrayExpressHTS, ArrayExpressHTSFastQ

Examples

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

ArrayExpressHTS documentation built on Nov. 17, 2017, 9:27 a.m.