Function reference • txtools

All functions

IUPAC_CODE_MAP_extended: IUPAC code extended to consider deletions

IUPAC_code_2nucs: IUPAC ambiguity alphabet (2nc)

IUPAC_code_simpl: Simplified nucleotide alphabet

annotSites_RRACH: RRACH sites annotation D. melanogaster

bam_sk1: Genomic Alignments example - Sk1 yeast

gA_sk1: Gene annotation example - Sk1 yeast

genome_sk1: Genome example - Sk1 yeast

getDumpedAlignments(): Retrieve dumped alignments

hid_aggregate_DTlist(): Merge lists of data.tables

hlp_coverageTab_mc(): Calculate coverage table (coverage, ends, starts) for all gene models without gene coordinates (Multicore)

hlp_genCoorTab_mc(): Coordinate system table generator

hlp_nucFreqTab_mc(): Calculate nucleotide frequency pileup for all gene models

hlp_plot_metageneRegions(): Plot an extracted metaGeneMatrix

mm_geneAnnot(): Download gene annotation - Case study # 2

sc_faGenome(): Download genome to temporary file - Case study # 1

sc_geneAnnot(): Download gene annotation - Case study #1

sc_rRNAmods_Taoka: Sk1 rRNA modifications catalogue

sc_txDTL: txtools-processed data - Case study # 1

tk_faGenome(): Download genome to temporary file - Case study # 3

tk_geneAnnot(): Download gene annotation - Case study # 3

txCoreCols: txtools' core cols

txCoreCols_refSeq: txtools' core cols and refSeq

txDTL_Tk: txtools-processed data - Case study # 3

tx_add_endRatio(): Add ends to coverage ratio 1 bp downstream

tx_add_endRatio1bpDS(): Add ends to coverage ratio 1bp down-stream

tx_add_endRatio1bpUS(): Add ends to coverage ratio 1bp up-stream

tx_add_exonNumber(): Add exon number

tx_add_exonPlace(): Add exon place

tx_add_geneRegion(): Add gene regions

tx_add_misincCount(): Add counts of nucleotide reads different to the reference sequence

tx_add_misincRate(): Add misincorporation to total nucleotide reads ratio

tx_add_misincRateNucSpec(): Nucleotide specific misincorporation rate

tx_add_motifPresence(): Add motif presence

tx_add_nucTotal(): Add total number of nucleotide reads

tx_add_pos(): Add position unique names

tx_add_refSeqDT(): Add reference sequence to a data.table

tx_add_relTxPos(): Add relative position in transcript

tx_add_rollingMean(): Add rolling mean

tx_add_siteAnnotation(): Add 1bp-site logical annotation

tx_add_spliceSitesLogical(): Add SpliceSites

tx_add_startRatio(): Add starts to coverage ratio

tx_add_startRatio1bpDS(): Add starts to coverage ratio 1 bp downstream

tx_add_startRatio1bpUS(): Add starts to coverage ratio 1 bp upstream

tx_complete_DT(): Complete a DT object missing genes

tx_counts(): Total counts of reads per gene model

tx_cutEnds_DT(): Cutting 5' and 3' ends of data.table using txcoors

tx_cut_geneAnnotBytxDT(): Cut gene annotation by txDT's genes

tx_data_caseStudy2(): Load data - Case study #2

tx_dm3_geneAnnot(): D. melanogaster gene annotation subset path

tx_extend_UTR(): Extending GRanges 5' and 3' UTR blocks

tx_filter_maxWidth(): Filter ranges by a maximum width

tx_generatePairedEndFASTQ(): Generate paired-end FASTQ file

tx_generateSingleEndFASTQ(): Generate single-end FASTQ file

tx_get_flankSequence(): Get flanking sequences

tx_get_flanksFromLogicAnnot(): Get data from a position and their neighboring positions

tx_get_geneLengths(): Get length of genes

tx_get_metageneAtCDS(): Get metagene at CDS

tx_get_metageneExons(): Get metagene by exons

tx_get_metageneRegions(): Get metagene regions

tx_get_transcriptSeqs(): Get transcriptome sequences

tx_get_unassignedAlignments(): Retrieve dumped alignments

tx_load_bam(): Read paired end bam file by yield size

tx_load_bed(): Load gene models from bed-12 and bed-6 files

tx_load_genome(): Load genome

tx_load_rdsDT(): Loading RDS files into data.tables

tx_makeDT_covNucFreq(): Summarized Coverage & Nucleotide Frequency data.table

tx_makeDT_coverage(): Summarized Coverage data.table

tx_makeDT_nucFreq(): Summarized Nucleotide Frequency data.table

tx_merge_DT(): Merge data.tables in list to a single data.table

tx_orderDT(): Order txDT

tx_plot_ggseqlogo(): Plot motif centered in logical annotation

tx_plot_metaGeneByBins(): Plot metagene by bins

tx_plot_metageneAtCDS(): Plot metagene at CDS

tx_plot_metageneExons(): Plot metagene exons

tx_plot_metageneRegions(): Plot metagene by regions

tx_plot_nucFreq(): Nucleotide frequency plot

tx_plot_numeric(): Numeric plot

tx_plot_staEndCov(): Transcript coverage plot highlighting read-starts and read-ends counts

tx_reads(): Transcriptomic reads convertion

tx_sampleByGenes(): Sample txDT by genes

tx_sample_GRList(): Sampling alignments

tx_shift_geneWise(): Shift column in txDT

tx_split_DT(): Split data.table to list of data.tables

tx_test_LRTedgeR(): Likelihood Ratio Test

tx_test_ttest(): t-test in txDT list

tx_unifyTxDTL(): Unify lists of txDTs

txtools txtools-package: txtools: A package facilitating analysis of RNA modifications, structures, and interactions

window_around(): Centered numeric sequence

tx_combineTxReads(): Combine txreads