Package index • tailquant

All functions

TailQuant-class: TailQuant class

calc_km(): Kaplan-Meier curve estimation

count_tails(): Count tail lengths

count_umis(): Count UMIs (or reads if UMIs not present)

demux_reads(): Demultiplex into FASTQ files from parquet file

ingest_read_pairs(): Initial loading and processing of Pooled PAT-Seq data into a parquet file

ingest_tt(): Ingest Tail Tools output

km_at(): Survival proportion for a specific tail length

km_quantile(): Quantile from a Kaplan-Meier curve

load_bam_into(): Load data from a BAM file

load_tt_sites(): Load site information from Tail Tools output

make_tests_oneway(): Make a set of tests with one experimental factor

make_tests_twoway(): Make a set of tests with one experimental factors

reads_peek(): Examine a random selection of reads

reads_report(): Reads report

scan_bam_chunks(): Scan GAlignments chunks

scan_parquet(): Scan a parquet file

site_reads_into(): Join reads to sites

tests_to_tt(): Convert tailquant test list to Tail Tools format

tq_export(): Tailquant data export as a set of parquet files

tq_plot_sample_tails(): Plot a distribution of tail lengths per sample (or group)

tq_proportions(): Get matrix of proprtion of tails as long or longer than a certain length

tq_quantiles(): Get matrix of quantile tail lengths

tq_shiny(): Shiny tailquant interface