Data Analysis

Permutations

Say we have the two following groups : g1 <- c(55, 65, 58) g2 <- c(12, 18, 32) We want to see if the two groups belong to the same distribution or can be considered as different groups. We might be tempted to try a Student’s t-test. t.test(g1, g2) ## Welch Two Sample t-test ## ## data: g1 and g2 ## t = 5.8366, df = 2.9412, p-value = 0.01059 ## alternative hypothesis: true difference in means is not equal [...]

By | 2016-11-08T09:30:09+00:00 October 14, 2015|Categories: Data Analysis, R, Statistics|0 Comments

Working with large files

When dealing with Next Generation Sequencing data, I am routinely asked by clients how to open sequence files. The answer is that given their huge size (often many million lines) and the consequent requirement in memory, they should probably not be opened in any way, they should only be processed. Most software designed to work with NGS data will then process these files in a sequential fashion or stream, loading just the required amount of data from disk, processing it [...]

By | 2016-11-08T09:30:09+00:00 October 1, 2015|Categories: Data Analysis, Shell scripting|1 Comment