Integrating Cap Enrichment with Transcript Expression Analysis

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Documentation for package ‘icetea’ version 1.27.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

activeChrs	Match BAM headers bw files and get active chromosome list (from restrict) (written by Aaron Lun, 12 Dec 2014, copied and modified here)
annotateTSS	Annotate the provided Transcription Start Sites
CapSet	Create a new CapSet object
CapSet-class	Create a new CapSet object
check_capSet	Check capset validity
demultiplexFASTQ	Demultiplex and tag fastq files using sample barcodes
demultiplexFASTQ-method	Demultiplex and tag fastq files using sample barcodes
detectDiffTSS	Detect differentially expressed Transcription Start Sites between two conditions (test)
detectDiffTSS-method	Detect differentially expressed Transcription Start Sites between two conditions (test)
detectTSS	Detection of Trancription start sites based on local enrichment
detectTSS-method	Detection of Trancription start sites based on local enrichment
diffQCplots	Make DESeq2 or edgeR QC plots
exampleCSobject	Create example CapSet object
exportTSS	Export the detected TSS from CapSet object as .bed files
exportTSS-method	Export the detected TSS from CapSet object as .bed files
filterDuplicates	Filter PCR-duplicates from mapped files using internal UMIs
filterDuplicates-method	Filter PCR-duplicates from mapped files using internal UMIs
filterDups	Filter PCR-duplicates from BAM file using internal UMIs
fitDiffTSS	Detect differentially expressed Transcription Start Sites between two conditions (fit model)
fitDiffTSS-method	Detect differentially expressed Transcription Start Sites between two conditions (fit model)
getBamFlags	Get flags to read from bam
getChromBins	Get chromosome bins from BAM files
getChromWindows	Get chromosome sliding windows from BAM files
getGeneCounts	Get gene-level counts from TSS data
getGeneCounts-method	Get gene-level counts from TSS data
getMCparams	Get platform-specific multicore params
getNormFactors	Calculate normalization factors from CapSet object
getNormFactors-method	Calculate normalization factors from CapSet object
getranks	Assign feature ranks on a VariantAnnotation output
get_newfastq	Get data to create new ShortReadQ object after barcode trimming
mapCaps	Map the data from 5' profiling techniques
mapCaps-method	Map the data from 5' profiling techniques
newCapSet	Create a new CapSet object
numReadsInBed	Count the number of reads in a given GRanges
plotPrecision	Plotprecision background script
plotReadStats	Plot read statistics from the CapSet object
plotReadStats-method	Plot read statistics from the CapSet object
plotTSSprecision	Compare the precision of TSS detection between multiple samples
plotTSSprecision-method	Compare the precision of TSS detection between multiple samples
readsTo3p	preprocess reads to count only 3' overlaps
readsTo5p	preprocess reads to count only 5' overlaps
readsToCenter	preprocess reads to count only center overlaps
sampleInfo	Retrieve and replace sample information of a CapSet object
sampleInfo-method	Retrieve and replace sample information of a CapSet object
sampleInfo<-	Retrieve and replace sample information of a CapSet object
sampleInfo<--method	Retrieve and replace sample information of a CapSet object
splitBAM_byIndex	Split the composite BAM file using internal indexes (MAPCap)
splitBAM_byRepindex	Split the composite BAM file using replicate indexes (MAPCap data)
splitranks	Get features with the best rank for each TSS
split_fastq	Split paired-end fastq by barcodes
strandBinCounts	Perform stranded Bin counts