extract_eic: extract_eic

View source: R/extract_eic.R

extract_eicR Documentation

extract_eic

Description

Extract EICs of some features from some samples.

Usage

extract_eic(
  targeted_table,
  object,
  polarity = c("positive", "negative"),
  mz_tolerance = 15,
  rt_tolerance = 30,
  threads = 5,
  add_point = FALSE,
  path = ".",
  group_for_figure = "QC",
  feature_type = c("pdf", "png"),
  width = 10,
  height = 6,
  device = NULL
)

Arguments

targeted_table

A data.frame contains the variable_id, mz and rt of features to extract.

object

object from xcms. If you use massprocesser, this should be the xdata3.

polarity

positive or negative.

mz_tolerance

default is 15 ppm.

rt_tolerance

default is 30 ppm.

threads

Number of threads.

add_point

aad points in the EIC or not.

path

Work directory.

group_for_figure

what samples groups are used to extract EICs

feature_type

png of pdf

width

figure width

height

height width

device

Device to use. Can either be a device function (e.g. png), or one of "eps", "ps", "tex" (pictex), "pdf", " jpeg", "tiff", "png", "bmp", "svg" or "wmf" (windows only).

Value

EICs.

Author(s)

Xiaotao Shen shenxt1990@outlook.com


tidymass/massprocesser documentation built on May 7, 2023, 10:18 p.m.