Function reference • brentlabRnaSeqTools

Data objects

data objects loaded with brentlabRnaSeqTools

database_info: URLS to active databases

grant_df: the 2016 grant summary represented as a dataframe

passing_genes_all: genes considered NOT to have 'high dispersion'

database_colnames: set global variables, mostly as a hack to make the tidyverse data binding pass the R CMD Check

Database – Utilities

Things like connecting directly to the database, archiving or retrieving a user token

connectToDatabase(): Connect to a remote postgresql database

archiveDatabase(): pull entire database (not counts) and save to output_dir for archival purposes

getUserAuthToken(): get (via a http POST request) your user authentication token from the database

Database – Getting Data

get the full join (getMetadata) or individual tables

getMetadata(): Get the combined metadata as a tibble from a remote database

getRawCounts(): Get combined raw counts

getGeneNames(): Get gene names

listTables(): list tables in databse

getTable(): Convenience function to pull a single table

getCapsuleImageSet(): Retrieve, as a zip file, the set of images which correspond to a given bioSampleNumber

Database – Sending Data

send data TO the database. Please be careful with these.

postFastqSheet(): post new fastq sheet to database

postCounts(): post counts to database

postQcSheet(): post new qc sheet to database

patchTable(): PATCH entries in database table

postTable(): Post a table to the database

postCapsuleJpeg(): Send a single JPEG KN99 capsule image to the capsule image table

postCapsuleJpeg_batch(): Send a set of JPEGs for a given bioSampleNumber to the database

postCountsToDatabase(): Send Counts to Database (legacy pipeline)

postImageAnnotationsToDatabase(): Send Capsule Image Annotation Data to Database

brentLabRnaSeq Object

the object(s) used in most of QC processing

brentlabRnaSeqExperiment(): brentlabRnaSeqExperiment constructor.

brentlabRnaSeqSet() brentlabRnaSeqSetFromDatabase(): brentlabRnaSeqSet object and constructor

brentlabRnaSeqSetTransform(): brentlabRnaSeqSetTransform object and constructor. This extends DESeqTransform.

coerceToDds(): coerce brentlabRnaSeqSet to DESeqDataSet

createExperimentSet(): Create a pre-defined experiment set

createTestTrainSet(): create test train set

estimateSizeFactorsByProtocol(): Calculate Size Factors within protocol groups

extractColData(): extract colData as tibble

extractDesignMatrix(): extract the model.matrix using the design and colData

getRunNumberLeadingZero(): correct run number to add leading zero where approprirate

qaFilter(): Quality filter a brentlabRnaSeqSet object

RNAseq Pipeline

Functions for processing data from the database for the RNAseq pipeline

readHTSeqFile(): Parse HTSeq output to tibble

parseNovoalignLog(): Parse a novoalign log

geneGRanges(): Given a GenomicFeatures annotation_db and a gene_id, extract an GRanges object of the cds

strandedScanBamParam(): A helper function to create a ScanBamParam object

htseq_proteinCodingTotal(): Calculate KN99 protein coding total

htseq_notAlignedTotalPercent(): Extract notAlignedTotalPercent from novoalign log

htseq_libraryComplexity(): Calculate percentage of library accounted for by top expressed genes

locusCoverage(): Calculate coverage over a given feature

htseq_locusLog2cpm(): Get the log2cpm of a given locus in the htseq output

novoalignPipelineQC(): QC a crypto run output by the novoalign+htseq pipeline

addQcColsToMeta(): add qc metrics to metadata

autoAuditQcTable(): Audit a qc table with metrics added

decomposeStatus2Bit(): decompose sums of powers of two to a list of the summed powers

kn99_novo_htseq_status: QC status codes for the novo+htseq pipeline

kn99_novo_htseq_thresholds: thresholds set for the novo+htseq pipeline

RNAseq Pipeline – nextflow

Functions for processing data in the nextflow pipeline

createNovoalignPipelineSamplesheet(): create a sample sheet for the novoalign pipeline

createNfCorePipelineSampleSheet(): create nf-co sample sheet

moveNfCoFastqFiles(): move fastq files from lts to scratch for nf-co/rnaseq pipeline

RNAseq QC – Misc

Miscellaneous RNAseq QC functions

setPerturbedLociToZero(): Zero out perturbed expression

removeParameterEffects(): remove some effects from the counts

fltrLowReplicateParams(): filter low replicate parameters from metadata

RNAseq QC – RLE

Functions used to calculate relative log expression for QC

rleTransform(): transform normalized counts into regularized log expression

calculateRLE(): calculate RLE of a numeric dataframe

calculateGeneWiseMedians(): calculate medians across rows of dataframe

rleSummary(): rleSummary calculates summary statistics of rleFullTable

addRleSummaryStats(): calculate RLE by replicate groups

rleByReplicateGroup(): calculate RLE by replicate groups

rlePlotCompareEffectRemoved(): plots output of rleSummaryByReplicateGroup

removeLibdateByReplicate(): Remove the libraryDate effects from KN99 dds objs

plotRLEhistograms(): composite plot of all rle_stats in one plot

rlePlot(): plot RLE for a given column filter

rlePlot_helper(): the actual plotting function for rlePlot

RNAseq QC – IGV

Functions for interacting with the IGV

createIgvBatchscript(): create IGV viewer batch script (single range, as many tracks as you like)

Experimental Sets

Functions for creating various pre-defined experimental sets

createEnvPertSet_perturbed(): create Environmental Perturbation Perturbed set

createEnvPertSet_titrationWT(): create Environmental Perturbation Titration (TDY451 only) set

createEnvPert_epWT(): filter combined_df for environmental perturbation sample set

createEPTally(): Create the EP tally in long form

createNinetyMinuteInduction_2016grant(): 90minuteInduction set Definition

createNinetyMinuteInduction_2016grantWithDoubles(): ninetyMin set where both doubles are in the grant_df

createNinetyMinuteInduction_all(): Samples with genotypes not in the grant_df

createNinetyMinuteInduction_non2016grant(): Samples with genotypes not in the grant_df

createInductionSetTally(): create 90 minute induction set tally

replicateByProtocolTally(): experimental replicates by libraryProtocol tally

replicateByProtocolTally_90min(): 90min replicate by protocol tally

filterWtByExperimentalLibdate_90min(): WT filtering helper for 90minInduction sets

splitProtocolGroups(): Split a brentlabRnaSeqSet into two by protocol

Binding Response EDA functions

For instance, for Rank-Response plots

rank_response_plot(): Given expresion and binding signal, plot the rank response a la doi:

create_partitions(): Given a vector length adn the size of each parition, create a vector which represents those partitions.

sort_rank_mean_expr(): Create a rank-response data frame

Utilities

Helper functions

isNumeric(): test if argument is numeric

is_integer64(): Test if value is datatype integer64

localView(): To view a data.frame / data.table in LibreOffice Calc

parseComparatives(): parse text comparative sentence

readInData(): read in columnar data

run_numbers_with_leading_zero: A named list containing a run number without a leading zero, eg 647, with the value being the same runnumber with a leading 0, eg 0647.

testBamPath(): test bam path