calpauseidx: Calculate Pause indeces for genes from a bam file

In yuabrahamliu/proRate: proRate is an R package to infer gene transcription rates with a novel least sum of squares method.

Calculate Pause indeces for genes from a bam file

Description

Calculate Pause indeces for genes from a bam file (Pause index is the ratio of transcription Polymerase II signal density near a gene promoter to signal density within the gene body, such that higher Pause indices reflect a greater enrichment of promoter-paused Polymerase II), and also plot the FPM value of each bp for specific genes.

Usage

calpauseidx(
  bamfile,
  genefile,
  genomename = NULL,
  tssradius = 1000,
  label = NULL,
  strandmethod = 1,
  savegenenames = NULL,
  plotgenenames = TRUE,
  threads = 1,
  genelencutoff = NULL,
  fpkmcutoff = 1
)

Arguments

bamfile	The bam file need to calculate the Pause indeces for genes. Can be a string indicating the directory of the file, or a GAlignmentPairs object, or a GRanges object from the original bam file.
genefile	The genes whose Pause indeces need to be calculated. If it is NULL, all the genes in the genome specified by the parameter genomename will be analyzed. If provied by the user, columns named as chr, start, end, strand, and gene_id are required. All genes should be longer than the maximum value of the parameters tssradius and genelencutoff.
genomename	Specify the genome of the genes to be analyzed, when the parameter genefile is NULL.
tssradius	A numeric value indicating the radius of the promoter region centering around the TSS
label	A string that will be included in the titles of the specific gene plots to indicate the experimental condition.
strandmethod	The strand specific method used when preparing the sequencing library, can be 1 for directional ligation method and 2 for dUTP method. If the sample is sequenced using a single strand method, set it as 0.
savegenenames	For which genes their concrete FPM value for each bp position need to be saved, or plotted.
plotgenenames	Whether to plot the FPM value for each bp position for the genes provided by the parameter savegenenames.
threads	Number of threads to do the parallelization. Default is 1.
genelencutoff	The cutoff on gene length (bp). The default value is NULL, but if it is set, only genes longer than this cutoff will be considerred.
fpkmcutoff	The cutoff on gene FPKM value. Only genes with an FPKM value greater than the cutoff will be considerred. Default is 1.

Value

Will generate a list containing a data.frame recording the Pause indeces of the genes, as well as plot the FPM value of each bp for the specific genes indicated by the parameter savegenenames.

yuabrahamliu/proRate documentation built on Nov. 3, 2024, 10:14 a.m.