In marziasettino/MMRFVariant: R package for variant analysis from MMRF-CoMMpass data source

MMRFVariant_SurvivalKM

Arguments | Description -----|----- patient|is the data.frame of the patient clinical data downloaded from MMRF-Commpass Researcher Gateway trt|is the data.frame of the patient clinical data (i.e. treatment-response) downloaded from MMRF-Commpass Researcher Gateway variant.ann| is the data.frame of the annotated variants downloaded from MMRF-Commpass Researcher Gateway Listvariant| is the list of the variants to analyze FilterBy| Column with groups to plot. This is a mandatory field. risk.table| show or not the risk table expand| show or not an expanded plot legend| Legend title of the figure xlim| x axis limits e.g. xlim = c(0, 1000). Present narrower X axis, but not affect survival estimates. main| main title of the plot labels| labels of the plot ylab| y axis text of the plot xlab| x axis text of the plot filename| The name of the pdf file. color| Define the colors/Pallete for lines. width| Image width height| Image height pvalue| show p-value of log-rank test conf.range| show confidence intervals for point estimates of survival curves. dpi| Figure quality

Survival Curves in the Stratified Patients Cohort

The KM survival curves are drawn with respect to the FilterBy parameter that can be set for stratifying the patients cohort into the categories shown in the following Table:

Arguments | Description -----|----- Ethnicity | Ethnicity Stage | ISS Stage Treatment | Treatment class Bestresp | Best overall response Gender | Female or Male Effect | Effect Type of observed mutation Biotype | Gene biotype

Example

The following plots show the KM survival curves for each variant (i.e. dbSNP ID) in "ListSNPs_NRAS" (we focus on NRAS gene) with respect to the:
- treatment (i.e. Therapy class)
- Stage
- Bestresp
- Ethnicity.
Note that Only the KM curves with pvalue$<$0.05 are shown. For simplification purposes, we take into account only the top five SNPs by occurrence.

Example

wzxhzdk:0 wzxhzdk:1

Resulting plot

wzxhzdk:2 wzxhzdk:3

Resulting plot

wzxhzdk:4 wzxhzdk:5

Resulting plot

wzxhzdk:6 wzxhzdk:7

MMRFVariant_GetImpact

Arguments | Description -----|----- variant.ann| is the data.frame of the annotated variants downloaded from MMRF-Commpass Researcher Gateway ListSNPs| is the list of the variants to analyze

Example

wzxhzdk:8 wzxhzdk:9

marziasettino/MMRFVariant documentation built on March 28, 2023, 3:16 p.m.