intSitesCART: CART insertion sites.

In Adrian-Cantu/gt34: What the Package Does (One Line, Title Case)

CART insertion sites.

Description

A dataset containing insertion sites for two CART patients across several timepoints.

Usage

intSitesCART

Format

A data frame with 13,066 rows and 28 variables:

seqnames

Chromosome

start

start position

end

end position (should be the same as start, it is here to be compatible with Granges)

width

width (should be 1, it is here to be compatible with Granges)

strand

which strand of DNA is the insertion located on

refGenome

reference genome

reads

Number of reads suporting this insertion site

patient

patien ID

GTSP

internal ID

cellType

Cell Type

timePoint

Time Point, free form format

timePointDays

Time Point (in days)

timePointMonths

Time Point (in months)

posid

Position ID in the format (Chromosome)(strand)(start)

estAbund

Number of unique clones, as define by SonicBreaks

relAbund

Relative abundance

inFeature

Whether the insertion is a gene

nearestFeature

Closes gene

nearestFeatureStrand

Strand of the nearest gene

inFeatureExon

whether the insertion is in an exon

inFeatureSameOrt

not sure...

nearestFeatureDist

Distance to nearest gene

nearestOncoFeature

Nearest Cancer related gene

nearestOncoFeatureDist

Distance to the nearest cancer related gene

nearestOncoFeatureStrand

Strand of the nearest cancer related gene

nearestlymphomaFeature

Neares Lymphoma related gene

nearestlymphomaFeatureDist

Distance to the nearest lymphoma related gene

nearestlymphomaFeatureStrand

Strand of the nearest lymphoma related gene

Source

Melenhorst, J.J. et al. (2022). Decade-long leukaemia remissions with persistence of CD4+ CAR T cells. Nature 1-7.

Adrian-Cantu/gt34 documentation built on March 24, 2022, 9:06 p.m.