Differential expression analysis
A paired differential expression analysis, i.e. post-vs-pre (one-month vs. baseline) comparison, was carried out for each study arm. For the paired analyses, only protein-coding probe-target genes were retained: hg19 probe coordinates from the Illumina RNA Exome kit were cross-mapped to hg38 genome assembly using cross-map, an assembly converter tool. Genes which are classified as ‘protein-coding’ by the gene biotype field in the hg38 GTF file and for which the exon coordinates showed an overlap of at least one base with any of the probe coordinates, were included in the set of protein-coding probe-target genes (19,543 genes). The overlap across the exon coordinates and probe coordinates was computed using the ‘closest’ tool from bedtools. DESeq2 (version 1.22.1) in Bioconductor/R platform was used to perform the differential expression analysis within the study arms, with a single-factor experimental design formula, design = ∼assigned_contraceptive [