Importing txt into Qfeatures

Overview

Teaching: 15 min
Exercises: 0 min

Questions

• How can we import txt file into QFeatures object?

• How can we add metadata to QFeatures?

• How can we inspect QFeatures features?

Objectives

• Import MaxQuant peptides.txt file into QFeatures object.

• Inspect QFeatures features.

Read peptide file into QFeatures

We can use the readQFeatures function from QFeatures package to import f data.frame that we read into R before. We also need to provide the position i where our quantitative Intensity columns live. We can name this new QFeatures object cptac.

library("QFeatures")
cptac <- readQFeatures(f, ecol = i, sep = "\t", name = "peptides", fnames = "Sequence")

Exercise

Use the colData function to see description of each sample from cptac

Solution

colData(cptac)

Encode the experimental design in QFeatures

We can update the sample (column) annotations to encode the two groups, 6A and 6B, and the original sample numbers.

ptac$group <- rep(c("6A", "6B"), each = 3)
cptac$sample <- rep(7:9, 2)
colData(cptac)

Get metadata information of QFeatures

We can get metadata information of QFeatures

rowData(cptac)

We can use the assay function to get a matrix-like cptac

library("magrittr")
assay(cptac) %>% head(2)

Key Points

• Functions from QFeatures and SummarizeExperiment packages allow to do these steps seamlessly.