# Integrating Cap Enrichment with Transcript Expression Analysis

## Documentation for package ‘icetea’ version 1.29.0

- 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