metaplot: Generate metagene plots 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.

Generate metagene plots from a bam file

Description

Generate metagene plots and other information from a bam file, such as the FPM value of each bp position in the metagene plots, FPKM values in specific TSS, TTS, or gene body regions of each gene, etc.

Usage

metaplot(
  metafile,
  targetgenefile = NULL,
  genomename = NULL,
  tssradius = c(2000, 1000, 500),
  ttsradius = c(2000, 1000, 500),
  genebodylen = 4000,
  label = NULL,
  strandmethod = 1,
  threads = 1,
  savegenenames = NULL,
  plotgenenames = TRUE,
  plotfig = TRUE,
  genelencutoff = NULL,
  fpkmcutoff = 1,
  textsize = 13,
  titlesize = 15,
  face = "bold"
)

Arguments

metafile	The bam file needed to generate the metagene plots. Can be a string indicating the directory of the file, or a GAlignmentPairs object, or a GRanges object from the original bam file.
targetgenefile	The genes whose FPM values need to be merged together to generate the metagene plots. If it is NULL, all the genes in the genome specified by the parameter genomename will be analyzed. If provided by the user, columns named such as chr, start, end, strand, and gene_id are required. All genes should be longer than the maximum value of the parameters tssradius, ttsradius, and genelencutoff.
genomename	Specify the genome of the genes to be analyzed, when the parameter targetgenefile is NULL. Can be "hg38" or "mm10".
tssradius	If want to plot the metagene in TSS region, should set this parameter as a vector with each element corresponding to a radius of the TSS region centering around the TSS site. Then, for each radius value, a metagene plot will be generated.
ttsradius	If want to plot the metagene in TTS region, should set this parameter as a vector with each element corresponding to a radius of the TTS region centering around the TTS site. Then, for each radius value, a metagene plot will be generated.
genebodylen	If want to plot the metagene in gene body region, set this parameter as a specific numeric value (bp). Because different genes have different gene body lengths, before merge their FPM values to the metagene, their gene body lengths should be scaled to a unified length, which is set by this parameter genebodylen. Genes with a longer length will be compressed to this gene length, and the ones with a shorter length will be exteneded.
label	A string that will be included in the title of the metagene plots to indicate the experimental condition.
strandmethod	Indicate the strand specific method used when preparing the sequencing library, can be 1 for the directional ligation method, 2 for the dUTP method, and 0 for a non-strand specific library. In addition, if the sample is sequenced using a single strand method, set it as 3.
threads	Number of the cores to perform parallelization. Default is 1.
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.
plotfig	Whether plot the metagenes or not. Default value is TRUE. For the genes indicated by savegenenames, only if both the parameters plotgenenames and plotfig are TRUE, they will be plotted.
genelencutoff	The cutoff on gene lengths (bp). The default value is NULL, but if it is set, only genes with a length longer than this cutoff will be considered for the metagene plotting.
fpkmcutoff	The cutoff on gene FPKM values. Only genes with an FPKM value greater than this cutoff will be considered. Default is 1.
textsize	The font size for the plot texts. Default is 13.
titlesize	The font size for the plot titles. Default is 15.
face	The font face for the plot texts. Default is "bold".

Value

Will generate several metagene plots as well as a list containing the information of the FPKM values on specific regions for each gene, the concrete FPM value on each bp position for the metagene plots, and the genes indicated by the parameter savegenenames, etc.

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