extract_eic: extract_eic

In tidymass/massprocesser: Comprehensitive tools for raw metabolomics data processing

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 [e-mail]

tidymass/massprocesser documentation built on Oct. 8, 2024, 10:32 p.m.