Package 'harbChIP'

utility function: get all hexamers in upstream sequence for an ORF

Description

utility function: get all hexamers in upstream sequence for an ORF

Usage

allhex(orf, usobj)

Arguments

orf	character string, ORF name
usobj	upstreamSeqs object

Details

computes Biostrings Views

Value

computes Biostrings Views

Author(s)

Vince Carey [email protected]

Examples

data(sceUpstr)
allhex("YAL001C", sceUpstr)

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workflow component – build an upstreamSeqs instance from a FASTA read

Description

workflow component – build an upstreamSeqs instance from a FASTA read

Usage

buildUpstreamSeqs2(fastaRead, organism="sce", provenance="harmen")

Arguments

fastaRead	results of a readFASTA from Biostrings
organism	string naming organism
provenance	string or structure describing provenance

Details

generates an instance of upstreamSeqs

Value

generates an instance of upstreamSeqs

Author(s)

Vince Carey <[email protected]>

Examples

# x = readFASTA(...)
# y = buildUpstreamSeqs2(x)

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analyze relationship between motif frequency and binding intensity for selected motif and TF

Description

analyze relationship between motif frequency and binding intensity for selected motif and TF

Usage

chkMotif4TF(motif, TF, chset, upstr, bthresh=2, countthresh=0)

Arguments

motif	character string in alphabet known to Biostrings
TF	name of a TF (sample name in the ChIP-chip data structure chset
chset	an ExpressionSet instance harboring ChIP-chip data
upstr	an instance of upstreamSeqs
bthresh	threshold for binding intensity results to declare TF 'bound' to the upstream region
countthresh	threshold for motif count to be considered 'present' in upstream region

Details

Uses countPattern to perform motif count.

Value

a list with elements call, table, and test, the latter providing the result of fisher.test

Author(s)

Vince Carey <[email protected]>

Examples

# slow
## Not run: 
data(harbChIP)
data(sceUpstr)
chkMotif4TF("CGGCCG", "RDS1", harbChIP, sceUpstr)

## End(Not run)

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Experimental Data Package: harbChIP

Description

binding ratios and intergenic region data from a ChIP-chip experiment in yeast

Usage

data(harbChIP)

Format

The format is: An ExpressionSetObject with covariates:

• txFac: transcription factor symbol from Harbison website CSV file columnnames

Note

derived from web site jura.wi.mit.edu/young_public/regulatory_code/GWLD.html, binding ratios

Examples

data(harbChIP)
  harbChIP
  experimentData(harbChIP)
  exprs(harbChIP)[1:6,1:7]
  dim(exprs(harbChIP))
  pData(featureData(harbChIP))[1:6,]

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Biostrings representations of S. cerevisiae upstream regions

Description

Biostrings representations of S. cerevisiae upstream regions

Usage

data(sceUpstr)

Details

environment-based S4 object with DNAstring elements

Value

environment-based S4 object with DNAstring elements

Author(s)

Vince Carey [email protected]

Examples

data(sceUpstr)
sceUpstr
getUpstream("YAL001C", sceUpstr)

---

Class "upstreamSeqs"

Description

Container for a collection of upstream sequences

Objects from the Class

Objects can be created by calls of the form new("upstreamSeqs", ...). Environments are used to store collections of DNAstrings.

Slots

seqs:

Object of class "environment" ~~

chrom:

Object of class "environment" ~~

revComp:

Object of class "environment" ~~

type:

Object of class "environment" ~~

organism:

Object of class "character" ~~

provenance:

Object of class "ANY" ~~

Methods

Nmers

signature(n = "numeric", orf = "character", usobj = "upstreamSeqs"): obtain all subsequences of length n as view elements of a DNA string

keys

signature(x = "upstreamSeqs"): ...

organism

signature(x = "upstreamSeqs"): ...

seqs

signature(x = "upstreamSeqs"): ...

show

signature(object = "upstreamSeqs"): ...

Author(s)

Vince Carey [email protected]

Examples

showClass("upstreamSeqs")
data(sceUpstr)
sceUpstr
keys(sceUpstr)[1:5]

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