small_trans: Transmission pairs iSNV

In jtmccr1/HIVEr: Analysis of transmission and intrahost iSNV data taken as part of the HIVE cohort

Description

A small silly example of transmission isnv comparision data.

Usage

small_trans

Format

a data frame with 12 rows of 35 variables

chr

Chromosome - genomic segment

pos

position on genomic segment

SPECID1

Specimen id for first sample

SPECID2

Specimen id for second sample

ENROLLID1

Enroll id for first sample

ENROLLID2

Enroll id for second sample

HOUSE_ID

Id of the house of the individual

onset1

The date of symptom onset for the first sample

onset2

The date of symptom onset for the second sample

transmission

The infered date of transmission

sequenced1

Logical - was the first sample sequenced

sequenced2

Logical - was the second sample sequenced

snv_qualified1

Did the first sample qualify for isnv identification

snv_qualified1

Did the second sample qualify for isnv identification

valid

Is this a valid transmission pair

double

Does this need to be analyzed in both directions

sequenced_pair

Did the whole pair get sequenced

titer_pair

Are both samples above the titer cut off (10^3)

snv_qualified_pair

Did both samples qualify for isnv detection

pair_id

Id for the pairing

quality_distance

Does the sample meet the distance criteria for a transmission pair

collect1

Date of collection for the first sample

collect2

Date of collection for the second sample

mutation

mutation as chr_refPosVar

ref

nucleotide in the plasmid control

var

nucleotide in the sample

pcr_result

qpcr result for the samples-Strain

freq1

The frequency of the variant in the first sample

freq2

The frequency of the vairant in the second sample

season

The season of sampling

gc_ul1

The genomes/ul in the first sample

gc_ul2

The genomes/ul in the second sample

freq

What benchmarking frequency do we consider this to be at

found

Is the variant found in the second sample

Source

data-raw/small_trans.R

jtmccr1/HIVEr documentation built on May 29, 2019, 1:50 a.m.