/chromosomal_abnormality

Primary LanguageHTML

This is a dada challenge project to detect aneuploidy, 2017 (possible packages deprecation).

Results include:

  1. PPT presentation, report in .html
  2. code in .Rmd
  3. a Rshiny app for interactive visualization, show values on hover
    open runShiny.R and follow instruction

Description

Aneuploidy is defined as presence of an abnormal number of chromosomes in a cell. We perform this test as part of our fertility panel.

We provided data of two batches (batch_1, batch_2) that include a number of samples with this abnormality. The objective of this data challenge is to estimate the number of X and Y chromosomes for each sample.

Each batch includes two files:

Depth:
This file has the average depth of each interval for each sample.

Interval_order:
This file has chromosome, start and end of the intervals in ‘Depth.csv’. The order of the rows in ‘Interval_order.csv’ file is the same as the order of the rows in ‘Depth.csv’ file in a given batch. Note that chromosomes X and Y are indexed as 23 and 24, respectively.

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