Description Usage Format References Examples
We downloaded a set of RNA-seq gene expression data from The Cancer Genome Atlas (TCGA). The data are sequenced on the Illumina GA platform with tissues collected from breast cancer subjects. In particular, we selected 28 samples from the tissue source site “BH”, which are controlled for white female subjects with the HER2-positive biomarkers. After data preprocessing based on nonspecific filtering, a total number of 11,453 genes are kept for subsequent analyses. Among these data are 12 pairs of matched tumor and normal samples, and 4 unmatched tumor samples. The sequencing depths of the selected samples range from 23.80 million reads to 76.08 million reads. In the proposed analysis, we inversely weigh the sequencing samples by their sequencing depths (per million reads).
1 | data("HER2")
|
The object HER2
is a list with the following elements:
dat
Data matrix with samples in rows and genes in columns. Column names are gene symbols.
Grp
Vector of group labels.
seq.depth
Vector of sequencing depth, corresponding to the rows of dat
.
Subj
Vector of subject IDs, corresponding to the rows of dat
.
The Cancer Genome Atlas (TCGA) https://cancergenome.nih.gov/.
Zhang et al. (2019) Highly efficient hypothesis testing methods for regression-type tests with correlated observations and heterogeneous variance structure. BMC Bioinformatics, 20:185.
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